Molecular modeling and docking of microbial inulinases towards perceptive enzyme-substrate interactions

Inulin is emerging as an extremely rare source of sugar, it is having more sweetening capacity than table sugar, has beneficial effect in diabetic patient. Inulinases mainly produced by the microorganism and it degrades inulin into fructose which is a digestible form. There are more than 58 strains of microorganisms which are involved in the production of inulinases. The present report investigates about the selectivity of inulin by inulinase and its action to produce fructose through molecular docking. We have investigated exo-inulinase and endo-inulinases from Penicillium sp. TN-88(BAC16218) and Penicillium sp. TN-88(BAA19132), respectively with different arrangement of amino acids in the active site which detect the substrate. The protein sequences described above were processed to homology modeling by Swiss model and further they were docked with 1-ketose and fructose-6-phosphate as substrate by DOCK6 software package (dock.compbio.ucsf.edu). The results of the present studies represented that fructose-6-phosphate ((2R,3R,4S) fructose-6-phosphate) was having better interaction with exo-inulinase showing grid score of -40.288094 and the conserved amino acid Asp-22, Asp 128, Asp 179 and Ser 84 of exo-inulinase are involved in the bonding. In addition to this it was also seen that 1-ketose ((3S,4R)-ketose 1-phosphate) did not shown any interaction with the conserved part of the endo-inulinase.