Structure and dynamics of alpha-glucosidase through molecular dynamics simulation studies

Abstract

Proteins have a vital role in the structure and function of biological entities. Enzymes are responsible for catalyzing many biochemical processes and at the same time enzyme inhibition studies have drawn attention for remedial purposes. The technique of molecular docking is employed to predict the structure of the intermolecular complex formed between the enzyme and its inhibitor. Alpha-glucosidase is a calcium containing enzyme. The inhibition of alpha-glucosidase enzyme is crucial for glycemic control. This is connected with AIDS treatment as it is recently reported that the viral glycoprotein synthesis depends upon the activity of the enzyme. The structural and functional details of alpha glucosidase enzyme have been studied using molecular dynamics simulation. Root mean square deviation (RMSD) values were calculated relative to the starting structure at 300K and at time t=0. Root mean square fluctuation (RMSF) values were calculated relative to the average structure obtained from the 300K simulation. The production run was performed at 300K under periodic boundary conditions for 5ns. Both root mean square deviation and fluctuation analyses indicated the presence of disorderedness of atoms along the glucosidase polypeptide chain.