De novo design of orthogonal peptide pairs forming parallel coiled-coil heterodimers

摘要

We used the principles governing the selectivity and stability of coiled-coil segments to design and experimentally test a set of four pairs of parallel coiled-coil-forming peptides composed of four heptad repeats. The design was based on maximizing the difference in stability between desired pairs and the most stable unwanted combinations using N-terminal helix initiator residues, favorable combinations of the electrostatic and hydrophobic interaction motifs and negative design motif based on burial of asparagine residues. Experimental analysis of all 36 pair combinations among the eight peptides was performed by circular dichroism (CD). On the basis of CD spectra, each peptide formed a high level of α-helical structure exclusively in combination with its designed peptide partner which demonstrates the orthogonality of the designed peptide pair set. A set of orthogonal peptides which, pairwise, form heterodimeric parallel coiled-coils have been designed on the basis of two requirements: exclusive formation of coiled-coil structure with its complement and by forbidding any other combination. The designed peptides were experimentally tested regarding pairing specificity and chemical/thermal stability.