Structural analysis of free and enzyme-bound amaranth alpha-amylase inhibitor: classification within the knottin fold superfamily and analysis of itsfunctional flexibility

The three-dimensional structure of the amaranth a-amylase inhibitor (AAI) a dopts a knottin fold of abcabc topology. Upon binding to a-amylase, it adop ts a more compact conformation characterized by an increased number of intr amolecular hydrogen bonds, a decreased volume and in addition a trans to ci s isomerization of Pro20. A systematic analysis of the 3-D structural datab anks revealed that similar proteins and domains share with AAI the characte ristic presence of proline residues, many of which are in a cis backbone co nformation. As these proteins fulfil a variety of functional roles and are expressed in very different organisms, we conclude that the structure of th e knottin fold, including the propensity of the cis bond, are the result of convergent evolution.