Crystal structures of designed armadillo repeat proteins: Implications of construct design and crystallization conditions on overall structure

Designed armadillo repeat proteins (dArmRP) are promising modular proteins for the engineering of binding molecules that recognize extended polypeptide chains. We determined the structure of a dArmRP containing five internal repeats and 3rd generation capping repeats in three different states by X‐ray crystallography: without N‐terminal His₆‐tag and in the presence of calcium (YM₅A/Ca²⁺), without N‐terminal His₆‐tag and in the absence of calcium (YM₅A), and with N‐terminal His₆‐tag and in the presence of calcium (His‐YM₅A/Ca²⁺). All structures show different quaternary structures and superhelical parameters. His‐YM₅A/Ca²⁺ forms a crystallographic dimer, which is bridged by the His₆‐tag, YM₅A/Ca²⁺ forms a domain‐swapped tetramer, and only in the absence of calcium and the His₆‐tag, YM₅A forms a monomer. The changes of superhelical parameters are a consequence of calcium binding, because calcium ions interact with negatively charged residues, which can also participate in the modulation of helix dipole moments between adjacent repeats. These observations are important for further optimizations of dArmRPs and provide a general illustration of how construct design and crystallization conditions can influence the exact structure of the investigated protein.