Cavitands are effective templates for inducing stability and nativelike structure in de Novo four-helix bundles

We have designed, synthesized and characterized eight cavitand-based de novo four-helix bundles, where each helix contains the basis sequence EELLKKLEELLKKG. We find that each de novo protein is highly helical and extremely stable to the chemical denaturant guanidine hydrochloride (GuHCl). We studied the effect of the cavitand-peptide linker on the stability of each de novo protein. Flexible linkers render the helical structures more susceptible to denaturation by GuHCl. Linker structure and length also dictate monomer/dimer equilibria of the proteins. Proteins containing 0-3 Cry units possess varying degrees of nativelike structure. In contrast, proteins containing two or four methylene Linkers are more characteristic of molten globules. These differences can be attributed to the additional hydrogen bonding capabilities of the glycine linker variants and to the distance between the cavitand template and the helical bundle. The cavitand pendent group was also changed in one de novo protein from a methyl group to a propyl-phosphate moiety. This alteration does not affect the stability or packing within the helical bundle; however, it does affect the monomer/dimer equilibrium.