Ankyrin Repeat Domain

The 5 Ankyrin repeat domains are in red. Each is a helical hairpin of two alpha-helices connected by a short turn. The ankyrin-domains are connected by longer loops. This ankyrin domain is part of ILK (integrin linked kinase.) It is found in complex with a PINCH LIM1 domain, in blue.


The structural basis of integrin-linked kinase-PINCH interactions.
Chiswell BP, Zhang R, Murphy JW, Boggon TJ, Calderwood DA.
Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):20677-82.

(PubMed)

3f6q (PDB)

Ankyrin repeat: a unique motif mediating protein-protein interactions.
Li J, Mahajan A, Tsai MD.
Biochemistry. 2006 Dec 26;45(51):15168-78. Review.

Abstract
Ankyrin repeat, one of the most widely existing protein motifs in nature, consists of 30-34 amino acid residues and exclusively functions to mediate protein-protein interactions, some of which are directly involved in the development of human cancer and other diseases. Each ankyrin repeat exhibits a helix-turn-helix conformation, and strings of such tandem repeats are packed in a nearly linear array to form helix-turn-helix bundles with relatively flexible loops. The global structure of an ankyrin repeat protein is mainly stabilized by intra- and inter-repeat hydrophobic and hydrogen bonding interactions. The repetitive and elongated nature of ankyrin repeat proteins provides the molecular bases of the unique characteristics of ankyrin repeat proteins in protein stability, folding and unfolding, and binding specificity. Recent studies have demonstrated that ankyrin repeat proteins do not recognize specific sequences, and interacting residues are discontinuously dispersed into the whole molecules of both the ankyrin repeat protein and its partner. In addition, the availability of thousands of ankyrin repeat sequences has made it feasible to use rational design to modify the specificity and stability of physiologically important ankyrin repeat proteins and even to generate ankyrin repeat proteins with novel functions through combinatorial chemistry approaches.

Tandem-repeat proteins: regularity plus modularity equals design-ability.
Javadi Y, Itzhaki LS.
Curr Opin Struct Biol. 2013 Aug;23(4):622-31. doi: 10.1016/j.sbi.2013.06.011. Epub 2013 Jul 4. Review.


Abstract
Researchers in the field of rational protein design face a significant challenge, which arises from the two defining and inter-related features of typical globular protein structures, namely topological complexity and cooperativity. In striking contrast to globular proteins, tandem repeat proteins, such as ankyrin, tetratricopeptide and leucine-rich repeats, have regular, modular, linearly arrayed structures which makes it especially straightforward to dissect and redesign their properties. Here we review what we have learnt about the biophysics of natural repeat proteins and recent progress in applying that knowledge to engineer the thermodynamics, folding pathways and molecular recognition properties of tandem repeat proteins, and we discuss the wealth of possibilities presented for the extension of this modular construction process to build new molecules for use in medicine and biotechnology.