Comparison of the effects of sucrose molecules on alcohol dehydrogenase folding with those of sorbitol molecules on alcohol dehydrogenase folding using molecular dynamics simulation

Abstract

Two molecular dynamics simulations of the protein ADH in solution at room temperature have been carried out, one in the presence (about 0.1 M) and one in the absence of sucrose. The results show that the sucrose molecules cluster and move toward the protein, and expel water from the protein surface. Also, coating by sucrose increases the conformational fluctuations of the protein compared to the sucrose-free system. In fact, at concentrated sucrose solution of 0.1 M, sucrose molecules accumulate around the protein surface and interact with ADH via many H-bonds, and form a continuous space-filling network. This network forms H-bonds with ADH and water molecules on the average distance of 5.5 and 11.9 Å, respectively. Actually, sucrose molecules have been located between water molecules and protein, while hydrogen bonding between sucrose–protein is less by about 19 % than that of sorbitol-protein. Also, hydrogen bonding between ADH and water molecules is decreased about 37 % in the presence of sucrose compared to sorbitol. Thus, it is expected that ADH folding is increased in the presence of sucrose molecules. It is finally concluded that Sucrose molecules form H-bond with water molecules by their polar groups, and the aromatic and nonpolar parts of sucrose molecules have the least share in interaction with ADA. Thus, functional groups of ADA are free and its flexibility and folding enhance in the presence of sucrose molecules. The latter fact is completely the reverse of sorbitol effect on ADA in moderately concentrated sorbitol solution.