Molecular Simulation Of Protein Adsorption On Carbonaceous Nanomaterials

The use of nano-materials with different properties to control,predict and utilize the protein adsorption,including orientation control,conformational conversion,etc.,can help us explore the general rule of biomolecule adsorption at the material interface,and help to solve a variety of key issues in different biological engineering applications.In this thesis,parallel tempering Monte Carlo(PTMC)and conventional all-atom molecular dynamics(MD)simulation method were adopted to study the inhibition effect of enzyme activity,conformational change,electron transfer and non-covalent immobilization of several proteins such as ?-chymotrypsin(?-ChT),HIV-1 regulatory protein,cytochrome c(Cyt c)and lipase on carbon-based nanomaterials like one-dimensional carbon nanotube(CNT),two-dimensional graphene and graphene oxide(GO),as well as three-dimensional graphite,so as to explore the interaction mechanism of proteins with different surfaces,and then through functional modifications to achieve the efficient application of materials.The thesis includes the following contents.1.The adsorption and enzymatic activities of ?-ChT on different carboxylated CNTs were studied by using PTMC and MD methods.The simulation results indicate that the adsorption and driving force of ?-ChT on different CNTs are contingent on the carboxyl group density.Meanwhile,only slight secondary structural changes are observed during the adsorption process.It is revealed that ?-ChT interacts with pristine CNT through hydrophobic forces and exhibits a non-competitive adsorption characteristic with the active site facing towards the solution;while it binds to carboxylized CNTs with the active pocket through a dominant electrostatic association,which causes the activity inhibition in a competitive mode.The inhibitory effect by functionalized CNT is mainly due to the spatial blockage of the active site of ?-ChT.These findings are consistent with experimental results and well explain the inhibition mechanism of ?-ChT at the molecular level.In addition,this study would help clarify the detailed mechanism of specific recognition and regulation of ?-ChT by other functionalized nanomaterials.2.The conformation transition of helical fragment of viral protein R(Vpr13-33)at water-graphene interface was explored by using MD method.The simulation results show that Vpr13-33 remains almost ?-helix structure in solution,but converted into ?-sheet structure when strongly adsorbed on the graphene surface by hydrophobic interactions.Meanwhile,the early stage of structure transition from ?-helical to ?-sheet is found;no complete and stable ?-sheet is observed in the studied time scale.Free energy landscape analysis further complements the transformation analysis of polypeptide conformation.The clustering analysis determines the most representative intermediate state.These findings are consistent with experimental results,and give a molecular level interpretation for the reduced cytotoxicity of Vpr13-33 to some extent upon graphene exposure.Meanwhile,this work will provide some insights into the detailed mechanism of graphene-induced protein conformation transition.3.The orientation of Cyt c adsorbed on the graphene and graphene oxide surfaces,conformational change,as well as the interaction characteristic and electron transport pathway were investigated by means of MD simulations.The results show that Cyt c adsorption onto GO surface is dominated by electrostatic attraction through positively charged lysine residues,whereas hydrophobic interactions contribute to the adsorption on the graphene surface.No significant structure alterations upon adsorption are occurred.On graphene,the heme plane of Cyt c tends to be horizontally oriented and far away from the surface,which is not conducive to electron transport.However,on the GO surface,the heme plane is slightly tilted to the normal direction of the surface;the axial ligand Met80 is closer to the surface,facilitating electron transfer.These findings can provide detailed information on the electron transfer mechanism of Cyt c with graphene-based materials and further improve and optimize the efficiency of bionic electronic devices.4.The adsorption mechanism and orientation of lipase on four surfaces with different chemical characteristics were studied by means of PTMC and MD simulations.It shows that lipase is strongly adsorbed onto the surface of hydrophobic graphite,as reflected by the large contact area and interaction energy.However,lipase adsorption onto the hydrophilic TiO2 surface is very weak and undergoes the desorption and reorientation processes due to two strongly adhered water layers.When adsorbed on positively and negatively charged surfaces(NH2-SAM and COOH-SAM),the orientation distributions of lipase are narrow;opposite orientations are obtained.Lipase adsorbed on NH2-SAM has its catalytic center oriented towards the surface,which is not conducive to the substrate binding;while the catalytic center faces toward the solution when adsorbed on the COOH-SAM.Besides,the native structures of lipase adsorbed on different surfaces are well preserved,which indicates lipase as a robust enzyme.The simulation results will promote our understanding on how surface properties of nanomaterials,such as charge or hydrophobicity,will affect lipase immobilisation,and help us for the rational design and development of immobilized lipase carriers.