title: Analysis of structural and physico-chemical parameters involved in the specificity of binding between alpha-amylases and their inhibitors.
abstract: Enzyme-inhibitor specificity was studied for alpha-amylases and their inhibitors. We purified and cloned the cDNAs of two different alpha-amylase inhibitors from the common bean (Phaseolus vulgaris) and have recently cloned the cDNA of an alpha-amylase of the Mexican bean weevil (Zabrotes subfasciatus), which is inhibited by alpha-amylase inhibitor 2 but not by alpha-amylase inhibitor 1. The crystal structure of AI-1 complexed with pancreatic porcine alpha-amylase allowed us to model the structure of AI-2. The structure of Zabrotes subfasciatus alpha-amylase was modeled based on the crystal structure of Tenebrio molitor alpha-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.
authors.affiliation: Laboratório de Biologia Molecular and Laboratório de Bioinformática, EMBRAPA, Recursos Genéticos e Biotecnologia, CP 02372, CEP 70770 Brasília, DF, Brazil.
authors.forename: M C
authors.initials: MC
authors.lastname: Da Silva
authors.forename: M F
authors.initials: MF
authors.lastname: de Sá
authors.forename: M J
authors.initials: MJ
authors.lastname: Chrispeels
authors.forename: R C
authors.initials: RC
authors.lastname: Togawa
authors.forename: G
authors.initials: G
authors.lastname: Neshich
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D003001:Cloning, Molecular; D001517:Coleoptera / Q000201:enzymology; D003196:Computer Graphics; D018360:Crystallography, X-Ray; D004791:Enzyme Inhibitors / Q000737:chemistry*; D007887:Fabaceae; D006860:Hydrogen Bonding; D037102:Lectins / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D037121:Plant Lectins; D010940:Plant Proteins / Q000737:chemistry*; D010946:Plants, Medicinal; D011487:Protein Conformation; D011994:Recombinant Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry; D016415:Sequence Alignment; D000516:alpha-Amylases / Q000037:antagonists & inhibitors* / Q000737:chemistry*
chemical_list: D004791:Enzyme Inhibitors; D037102:Lectins; D037121:Plant Lectins; D010940:Plant Proteins; D011994:Recombinant Proteins; C061510:alpha-amylase inhibitor, Phaseolus vulgaris; D000516:alpha-Amylases