Molecular basis for the specific binding of different alpha-amylase inhibitors from Phaseolus vulgaris seeds to the active site of alpha-amylase

In search of a possible mechanism of inhibition which might be responsible for the different specificities of the three isoforms of the bean (Phaseolu s vulgaris) alpha-amylase inhibitor alpha-AI1, alpha-AI2 and alpha-AIL (EC 3.2.1.1), the two isoforms alpha-AI2 and alpha-An, were modelled from the a tomic co-ordinates of alpha-AI1 in the alpha-AI1/PPA complex and docking ex periments were performed with pig pancreatic alpha-amylase (PPA) and the mo delled amylase from Zabrotes subfasciatus (ZSA). The modelled alpha-AI2 pen etrates without any steric hindrance in the substrate cleft of both enzymes but the possible hydrogen bonds between PPA and alpha-AI2 seem too few to maintain the stability of the complex. alpha-AIL, which differs from alpha- AI1 and alpha-AI2 by the absence of post-translational proteoIytic cleavage and the occurrence of two additional loops of fifteen and six residues, cr eates steric clashes with PPA and ZSA that prevent its penetration into the substrate cleft of the enzyme. Docking experiments explain at the molecula r level the specificity of alpha-amylase inhibitor isoforms towards enzymes of different origins. In addition, they explain why, according to its unpr ocessed and more bulky character, alpha-AIL was previously shown to be inac tive on all alpha-amylases assayed. In fact, this last isoform is now consi dered as an evolutionary intermediate between phytohaemagglutinins, arcelin s and alpha-amylase inhibitors. (C) 2000 Editions scientifiques et medicale s Elsevier SAS.