MD Simulation Research On Interations Between Water Clusters And Protein

In recent years, the exploration of small-scale water clusters on its physical and chemical properties has become a hot field in cluster research, such as structure, molecular behavior, H-bond network etc. The weak role of water clusters exists in biological macromolecules system. Research on the indirect solvent environment of biological systems is expected to provide favorable basis for revealing natural problems in fields of Chemistry, Life Science, Information Science etc.This paper has studied effects of different solvents on protein-model-Lysozyme and researched the dynamic properties of lysozyme in Lysozyme-water (L-W) and Lysozyme-water clusters (L-WC) systems. It is the groundwork for futher research on the mechanism of interaction between AQPs and water clusters.MD simulation of L-W systems has shown that lysozyme in normal water displays conformational stability. Weak hydrogen bonding interactions have been found between lysozyme and water solvent mostly in spite of H-Bond interaction between leucine 129 and water molecule and between alanine 82 and water molecule. Aside, the distribution of water molecules around lysozyme is looser than pure water. The watershell analysis of serine 91 and valine 92 has confirmed that serine 91 is an active site in the non-polar cavity.MD simulation of L-WC systems has shown that hydrogen bonding interactions are more common and the conformation of lysozyme has changed significantly because of solvation effects of water clusters, with -helix dispersing, the three-class structural damaged and protein losing activity, all the results have explained the foregoing conclusion in theory that nano-water clusters can inhibit the growth of Escherichia Coli. Radial distribution function and watershell analysis shows that small-scale water clusters mainly distribute in the first hydration layer around lysozyme, and arrange loosely.In summary, the solvent effects of water clusters and normal water on lysozyme are quite different. Small-scale water clusters have damaged the protein conformation. This paper has layed on foundation for further explanation for the impact of water clusters on biochemical reactions.