Assessing the integrity of designed homomeric parallel three-stranded coiled coils in the presence of metal ions

Abstract

De novo design of alpha-helical peptides that self-assemble to form helical coiled coils is a powerful tool for studying molecular recognition between peptides/proteins and determining the fundamental forces involved in their folding and structure. These amphipathic helices assemble in aqueous solution to generate the final coiled coil motif, with the hydrophobic residues in the interior and the polar/hydrophilic groups on the exterior. Considerable effort has been devoted to investigate the forces that determine the overall stability and final three-dimensional structure of the coiled coils. One of the major challenges in coiled coil design is the achievement of specificity in terms of the oligomeric state, with respect to number (two, three, four, or higher), nature (homomers vs heteromers), and strand orientation (parallel vs antiparallel). As seen in nature, metal ions play an important role in this self-organization process, and the overall structure of metalloproteins is primarily the result of two driving forces: the metal coordination preference and the fold of the polypeptide backbone. Previous work in our group has shown that metal ions such as As(III) and Hg(II) can be used to enforce different aggregation states in the Cys derivatives of the designed homotrimeric coiled-coil TRI family [Ac-G(LKALEEK)4G-CONH2]. We are now interested in studying the interplay between the metal ion and peptide preferences in controlling the specificity and relative orientation of the alpha-helices in coiled coils. For this objective, two derivatives of the TRI family, TRi L2WL9C and TRi L2WL23C, have been synthesized. Along with those two peptides, two derivatives of Coil-Ser, CSL9C and CSL19C (CS = Ac-EWEALEKKLAALESKLQALEKKLEALEHG-CONH2), a similar de novo designed three-stranded coiled coil that has the potential to form antiparallel coiled coils, have also been used. Circular dichroism, UV-vis, and 199Hg and 113Cd NMR spectroscopy results reveal that the addition of Hg(II) and Cd(II) to the different mixtures of these peptides forms preferentially homotrimeric coiled coils, over a statistical population of heterotrimeric parallel and antiparallel coiled coils.