Pe Surface Phospholipids, Peptides, Weak Interaction Molecular Modeling

Surface interactions are extremely significant in scientific research and industrial applications. Forexample, some biomolecules, such as lipids, proteins, amylase etc. the interactions betweenbiomaterials surface and those molecules are the key point to design and develop biomaterials.However, at present, it is difficult to investigate the interaction energy and interaction mechanism byexperimental approaches at the single molecular level. With the development of computertechnology, software and their application in chemical research, it has enormously potential atinvestigating surface interactions and microcosmic mechanism by molecular simulation.Themethods have been widely used in materials design and drug discovery. In our work, moleculardynamic simulation was applied to investigate the adsorption process and interactions betweenpeptide segments, lipids and PE SAMs terminated with functional groups. How to describe ourexperimental model, how to model it by computer simulation method as well as the simulationtechniques used in different situations and system, and the parameters settings were discussed in ourwork. We also introduced some methods to analyse the dynamics trajectory, to investigate theinteraction process and the mechanism from the results. To sum up, by investigating this problem,we want to summarize the approaches and theories developed in the molecular simulation briefily,and hope this work will be helpful to the surface interactions researching and molecular design.The dynamics simulation was done by Material Studio software package. NVT esamble and CVFF,CFF91 force field were used. The Mulliken charge was obtained from force field assignment andquantum calculation. The molecular dynamics process of1,2-dimyristoyl-sn-glycero-phosphatidylcholine(DMPC) and PE SAM terminated with -CH₃,-OH, -CO, -COOH, -COO(?) in vacumm and aqueous solution, Glycine tetra-peptide segments andPE SAMs terminated with -CH₃, -NH₂, -OH, -COOH, -COO(?) in aqueous solution wereinvestigated by molecular dynamics simulation in Discover model of MS. Aimed at, on one hand, toget the information about the interaction relationship between different functional groups andbiomolecues and conformational change of biomolecues, on the other hand, to find the right model and simulation methods.By investigateing the interactions between DMPC and PE SAM surface terminated with -CH₃,-OH, -CO, -COOH, -COO(?) in vacuum and anqueous system. The results of nonbond interactionenergy, the Radial Distribution Function (RDF) and probability analysis show that the stronginteraction exist between DMPC and -CO, -COOH, -COO(?) terminated surfaces, and the key factorof interaction is the Coulomb electionic interaction of charged surface. The interaction between DMPC and -OH, -CH₃ terminated surfaces are very weak.Meanwhile by investigateing the interactions between Glycine tetra-peptide segments and PESAM surface terminated with -NH₂, -CH₃, -OH, -COOH, -COO(?) in anqueous system, the resultsof nonbond interaction energy, RDF, torsion angle analysis show that the strong interaction existbetween Glycine tetra-peptide and -COOH, -COO(?) terminated surfaces, the conformation of peptidewas strongly influenced by the amount of charge of surface; The simulation results of 9 differentkinds of optimized Glycine tetra-peptides interaction on the -COOH PE SAM show that stretchedconformations can be well affinity on this kind of charged surface.Combined with the experimental results of literatures and our own. The result of this simulationresearch can be concluded that by controlling the amount of negative charge on the materials surfaceand hydrophilic of the surface can be in fovor of controlling the biocompability and target orientedmolecular design by molecular simulation.