We describe the synthesis and characterization of novel isoleucine zipper polypeptide dimers, connected with a maleimide-containing linker molecule, that can assemble into structurally defined heterotrimeric -helical coiled coil dimers on the basis of architectural features of the polypeptide sequences. Linear-and crosslinked-isoleucine zipper polypeptide dimers were designed in this study. Circular dichroism spectroscopy, gel filtration, and HPLC analyses indicate that each polypeptide dimer can noncovalently assemble with four isoleucine zipper polypeptides and lead to heterotrimeric -helical coiled coil dimer formation. Thus, we concluded that monodispersed dimerization of triplestranded coiled coil was achieved for the first time. Moreover, the noncovalently assembled supramolecule may be useful as a the building-block for constructing artificial polypeptide fibrillogenesis systems.Noncovalent interactions of native proteins play an important role in supramolecular assembly and biological activity. Therefore, there is great interest in the rational design of self-assembled polypeptides. Among these designed polypeptides, fibrous polypeptides are important motifs for biological and nanotechnological applications. Up to now, several polypeptides including -helix and -sheet structure units have been designed for constructing well-defined fibrous supramolecular assemblies. Although self-assembling fibrils derived from -sheet motifs have been widely investigated as nanoarchitecture, 1-4 the design of -helical-assembled fibrils is not as advanced. 5-7-Helical scaffolds differ in critical structural features such as the periodic long axis of the fibril, from -sheet assemblies.This suggests that helical protomers are considered as complementary modules to -strands for the development of functional nanoscale materials. Moreover, in contrast to amyloidogenic polypeptides, the principles that govern the association ofhelical protomers into discrete coiled coil assemblies 8 have been elucidated in detail from structural studies on model polypeptides, such as leucine zippers 9-12 and isoleucine zippers. 10,11,13 However, the potential of these -helical coiled coil polypeptides for the construction of well-defined fibril structures remains largely untapped in spite of the fact that fibrious structures derived from -helical coiled coil motifs are formed widely in native biological systems, such as cytoskeleton and extracellular matrix.14 Thus, -helical motifs are an attractive target for de novo design of well-defined fibrils from self-assembly of synthetic helical protomers.We have reported an AAB-type-heterotrimeric -helical coiled coil by mutation of one amino acid residue at the hydrophobic a position of an isoleucine zipper polypeptide. [15][16][17] In our design, two kinds of amino acids with different side chain sizes have been used. One Ala residue at the hydrophobic a position destabilizes the formation of the coiled coil trimer, because of the small size of its side chain. On the other hand, Trp residue is though...