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

Enzyme-inhibitor specificity was studied for alpha-amylases and their inhib itors, We purified and cloned the cDNAs of two different alpha-amylase inhi bitors from the common bean (Phaseolus vulgaris) and have recently cloned t he cDNA of an alpha-amylase of the Mexican bean weevil (Zabrotes subfasciat us), which is inhibited by alpha-amylase inhibitor 2 but not by alpha-amyla se inhibitor 1. The crystal structure of AI-1 complexed with pancreatic por cine alpha-amylase allowed us to model the structure of AI-2. The structure of Zabrotes subfasciatus alpha-amylase was modeled based on the crystal st ructure of Tenebrio molitor alpha-amylase, Pairwise AI-l 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 com plex formation. The parameters we studied provide insight into the general scheme of binding, but fall short of explaining the specificity of the inhi bition. We also introduce three new tools - software packages STING, HORNET and STINGPaint - which efficiently determine the interface forming residue s and the ionic interaction data, the hydrogen bond net as well as aid in i nterpretation of multiple sequence alignment, respectively.