COMPUTATIONAL ANALYSIS OF THE STRUCTURAL PROPERTIES OF ALPHA - AND BETA - GALACTOSIDASES
Keywords:
global and local structural properties, surface cavities; surface roughness.Abstract
A computational study to compare the global and local physicochemical and structural properties of alpha- and beta-galactosidases using the retaining catalytic mechanism was performed. These proteins share quite similar global structural properties despite their low sequence similarity, structures superposition resulting in root mean squared deviation (RMSD) values around 1.25 Å for at least 43 alpha carbon atoms pairs. Almost the same RMSD values are obtained for the superposition of the catalytic domains of investigated galactosidases, but for a higher number of alpha carbon atoms pairs (68) reflecting the higher structural similarity of the catalytic domains. There are local individual properties of the surfaces of considered enzymes, beta-galactosidases exposing a more complex surface with a higher number of cavities, 42 for eukaryotic beta-galactosidases compared to 18 for eukaryotic alpha-galactosidases. Furthermore, beta- galactosidases usually depict larger and more hydrophobic cavities than alpha – galactosidases, the hydrophobicity scores of the biggest cavities being 24 for eukaryotic beta-galactosidases and 7 for eukaryotic alpha-galactosidases, respectively.
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