Molecular dynamics simulations of glycolipid and carbohydrate binding protein systems in the explicit water environment

Abstract

The carbohydrate derivatives as naturally embedded systems on the cell membrane lipids and proteins are regarded as flexible molecules with wide array of conformations and protein recognition functions. These groups have been awarded an increasing interest in the recent years due to the mounting evidence that they mediate a host of functions including protein-carbohydrate interaction, cell type recognition, cell signaling and development as well as differentiation. Many questions concerning the protein-carbohydrate interactions are therefore associated with conformational behavior of these biomolecules. Even though experiments provide valuable information about the specificity, binding affinities and other equilibrium thermodynamic properties, it is not always possible to exactly characterize the binding region and the forces involved in such bindings. The dynamics involved in these binding processes are of paramount importance, giving way to the flexible adaptive structures in the solution. Because of the intrinsic dynamics bound with the carbohydrate molecules, not all of the required information can be readily obtained from the experimental studies, so theoretical approach is the only alternative to supplement the experimental data.