Subsite mapping of the binding region of α-amylases with a computer program

Abstract

A computer program has been evaluated for subsite map calculations of depolymerases. The program runs in Windows and uses the experimentally determined bond cleavage frequencies (BCFs) for determination of the number of subsites, the position of the catalytic site and for calculation of subsite binding energies. The apparent free energy values were optimized by minimization of the differences of the measured and calculated BCF data. The program called Suma (SUbsite Mapping of α-Amylases) is freely available for research and educational purposes via the Internet (E-mail: gyemant@tigris.klte.hu). The advantages of this program are demonstrated through α-amylases of different origin, e.g. porcine pancreatic α-amylase (PPA) studied in our laboratory, in addition to barley and rice α-amylases published in the literature. Results confirm the popular 'five subsite model' for PPA with three glycone and two aglycone binding sites. Calculations for barley α-amylase justify the '6 + 2 + (1) model' prediction. The binding area of barley α-amylase is composed of six glycone, two aglycone binding sites followed by a barrier subsite at the reducing end of the binding site. Calculationsfor rice α-amylase represent an entirely new map with a '(1) + 2 + 5 model', where '(1)' is a barrier subsite at the nonreducing end of the binding site and there are two glycone and five aglycone binding sites. The rice model may be reminiscent of the action ofthe bacterial maltogenicamylase, that is, suggesting an exo-mechanism for this enzyme.