Structures of designed armadillo-repeat proteins show propagation of inter-repeat interface effects

The armadillo repeat serves as a scaffold for the development of modular peptide-recognition modules. In order to develop such a system, three crystal structures of designed armadillo-repeat proteins with third-generation N-caps (Y-III III-type), four or five internal repeats (M-type) and second-generation C-caps (A(II II)-type) were determined at 1.8 angstrom (His-Y(III III)M(4 4)A(II II)), 2.0 angstrom (His-Y(III III)M(5 5)A(II II)) and 1.95 angstrom (Y(III III)M(5 5)A(II II)) resolution and compared with those of variants with third-generation C-caps. All constructs are full consensus designs in which the internal repeats have exactly the same sequence, and hence identical conformations of the internal repeats are expected. The N-cap and internal repeats M-1 1 to M-3 3 are indeed extremely similar, but the comparison reveals structural differences in internal repeats M-4 4 and M-5 5 and the C-cap. These differences are caused by long-range effects of the C-cap, contacting molecules in the crystal, and the intrinsic design of the repeat. Unfortunately, the rigid-body movement of the C-terminal part impairs the regular arrangement of internal repeats that forms the putative peptide-binding site. The second-generation C-cap improves the packing of buried residues and thereby the stability of the protein. These considerations are useful for future improvements of an armadillo-repeat-based peptide-recognition system.