Analysis of structural and physico-chemical parameters involved in the specificity of binding between α-amylases and their inhibitors

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Abstract
Enzyme–inhibitor specificity was studied for α-amylases and their inhibitors. We purified and cloned the cDNAs of two different α-amylase inhibitors from the common bean (Phaseolus vulgaris) and have recently cloned the cDNA of an α-amylase of the Mexican bean weevil (Zabrotes subfasciatus), which is inhibited by α-amylase inhibitor 2 but not by α-amylase inhibitor 1. The crystal structure of AI-1 complexed with pancreatic porcine α-amylase allowed us to model the structure of AI-2. The structure of Zabrotes subfasciatus α-amylase was modeled based on the crystal structure of Tenebrio molitor α-amylase. Pairwise AI-1 and AI-2 with PPA and ZSA complexes were modeled. For these complexes we first identified the interface forming residues. In addition, we identified the hydrogen bonds, ionic interactions and loss of hydrophobic surface area resulting from complex formation. The parameters we studied provide insight into the general scheme of binding, but fall short of explaining the specificity of the inhibition. We also introduce three new tools—software packages STING, HORNET and STINGPaint—which efficiently determine the interface forming residues and the ionic interaction data, the hydrogen bond net as well as aid in interpretation of multiple sequence alignment, respectively.