Molecular Dynamics Simulations Of Protein Adsorption On Material Surface

Protein interacted with materials and spontaneously adsorbed to the surface is a widespread phenomenon in nature. In many cases, protein adsorption is advantageous, but more often, protein adsorption at the surface will bring undesirable results. Especially biofouling due to adhesion of marine organisms occurring in the marine environment, it can accelerate corrosion of metal equipment operations in the sea, affects the normal use of the facility, increases the resistance of the ship sailing in the sea and will makes the meter or rotating machine malfunction, etc. Generally, early marine biofouling is mainly caused by mucous proteins adsorption on the surface which secreted by marine organisms. Therefore, research the protein conformationals^ changes in the interaction process, mechanism of action and different materials’ influences will help us understand and make use of it to improve existing methods of production, to find better antifouling material.In this thesis, we adopted molecular simulation method to research the mechanisms of proteins’ adsorption on materials. Compared with the traditional experimental methods, molecular dynamics simulations could greatly reduce the blindness and revision test time-consuming of experiments. In additional, molecular simulation can not only provide a clear three-dimensional structure picture of the protein conformationals changes in studied systems, but also allow us to have greater awareness on that the influence of the surface properties of the materials on protein adsorption in order to find a better anti-fouling materials. The specific research contents are listed as below.(1) Molecular dynamics simulations were used to compare the adsorption behavior of lysozyme on two typical antifouling polymer materials:poly(ethylene) glycol (PEG) and poly(dimethylsiloxane) (PDMS). The influence of the surface properties of the polymer films on protein adsorption is discussed at the microscale. Based on the interactions, energy changes between the protein and polymer films, and dynamical behavior of the hydration molecules near the polymer film, the results were determined as follows:The lower binding energy between the protein and the PEG coating than between the protein and the PDMS coating makes the protein adsorb weaker on the PEG coating than on the PDMS coating; The protein would adsorb on the film surface when overcoming the energy barrier caused by the hydration layer, molecular water adsorbs on the PEG surface stronger than on the PDMS surface, and is difficult to desorb. Therefore, the protein needs to overcome a higher energy barrier to adsorb to the PEG surface than to the PDMS surface, and these are the reasons why the PEG antifouling coating has a better antifouling effect than the PDMS surface.(2) The interactions between protein with self-assembled monolayer films (SAMs) with different terminal functional groups were studied by molecular dynamics method. For their surface structures and chemical properties can be adjusted by changing the surface composition and terminal functional group, and it can be well characterized at the molecular scale, SAMs are ideal platform for the study of the interface behavior of protein. Firstly, we analyzed the interactions between protein lysozyme with hydrophobic CH3-SAMS and hydrophilic CH2OH-SAMS and COOH-SAMs, then the studied of parameter variations of protein and dynamical behavior of water molecule on the surface in contrast, conclusions were draw that protein lysozyme has the maximum interaction energy with hydrophobic CH3-SAMS and it has larger deformation, it is beneficial for protein adsorption and difficult for its own desorption; hydrophilic SAMs surface bond with hydration layer molecules more closely, so it’s hard for protein adsorption for overcoming higher energies, compared with COOH-SAMs, CH2OH-SAMS has stronger protein-resistant and anti-fouling ability.(3) Molecular dynamic simulations were performed to study the adsorption of hydrophobin on the surface of the silica at the air/water interface. Hydrophobic protein is currently known to have the strongest surface active and it can reduce the surface tension which can form a layer of protective film and produce spores after adsorption. This has an important contribution to the early formation of biological membrane of marine biological pollution. We studied adsorption conditions, and conformational changes of proteins when the hydrophobic protein is placed in the silica surface from different directions (each direction of rotation 90 °) in order to reveal the mechanism of adsorption phenomenon between rock surface and the protein in marine environment. The results show that:The orientation of placement will influence adsorption, even adsorption phenomenon does not occur. Besides, protein flip vary throughout the kinetics of absorption and final configurations are different. We did a survey of the type of amino acid adsorbed and found that a large proportion of hydrophobic amino acids among total amino acids adsorbed; At the same time, we analyzed protein’s configuration parameters-radius of gyration and the root mean square deviation. They have little difference which tells us different placements have little effect on proteins conformational changes and the hydrophobin has no denaturation phenomenon in the simulation time; After compared the energy changes of the 4 systems, we discovered that the amount of energy is relevant to the type of amino acid adsorbed on the surface, moreover, the systems which adsorbed more closely between protein and SiO2 substrate after dynamics have higher energy.