Computer Simulations Of Redox Protein Adsorption On Functionalized Nanomaterials

The immobilization of redox proteins on the surface of nanomaterials has a wide range of applications in the fields of biosensors and biofuel cells.Therefore,the adsorption mechanism of redox proteins on different nanomaterial surfaces was studied to reveal the general rules of the influence of material surface functionalization on protein adsorption.It is very important for improving the efficiency of protein immobilization and enzyme activity on different nanomaterial surfaces,and can provide practical theoretical guidance for the design and development of high-efficiency and low-cost enzymatic biofuel cells and highly sensitive enzyme biosensors.In this dissertation,a multi-scale simulation method,which combined the parallel tempering Monte Carlo?PTMC?and all-atom molecular dynamics?AAMD?,is used to study the adsorption mechanism of Myrothecium verrucaria bilirubin oxidase?Mv BOx?and acetylcholinesterase from Torpedo californica?Tc ACh E?on different materials,including the amino-terminated and carboxyl-terminated self-assembled monolayer?SAMs?,graphene?GRA?,graphene oxide?GO?,reduced graphene oxide?RGO?,carbon nanotube?CNT?,amino-modified CNT?CNT-NH₂?and carboxyl-modified CNT?CNT-COOH?.The regulation mechanism of surface charge density?SCD?and the functionalization of nanomaterials on protein adsorption orientation was revealed,and the general laws of the influence of protein properties?i.e.,charge properties,hydrophobicity,electric dipoles,and hydrophobic dipoles?on protein adsorption behavior were also explored.The main content and findings of the dissertation are as follows:1. The AAMD simulations combined with PTMC simulations have been employed to explore the orientation,conformation and the efficient direct electron transfer?DET?of Mv BOx on oppositely charged SAM surfaces with different surface charge densities(±0.05 C·m^-2 and±0.19 C·m^-2).Simulation results show that the negatively charged surface is beneficial for DET with the T1 copper site close to the electrode surface;while it is always far away from the surface once Mv BOx adsorbs on positively charged surfaces.Furthermore,the negatively charged surface with low SCD is more suitable for the DET between Mv BOx and electrode.Although Mv BOx is a negatively charged protein,it can stably adsorb on negatively charged surfaces and obtain a good adsorption orientation for DET.2. The adsorption orientations and conformations of Mv BOx on the GO,RGO and GRA surface were studied at the molecular level by using the multi-scale molecular simulation method?AAMD combined with PTMC?.The effects of SCD and surface hydrophobicity of GRA-based nanomaterials on the adsorption behavior of Mv BOx were revealed.The results show that Mv BOx is adsorbed on the GO and RGO surfaces with almost the same orientation,i.e.,its T1 copper sites orient and close to the surface.The difference is that when adsorbed on the RGO surface,the distance between the T1 copper site of Mv BOx and the surface is shorter than that on the GO surface,which indicates that the negatively charged RGO surface with lower SCD is more conducive to the DET process of Mv BOx on the electrode surface.On the GRA surface,the T1 copper site is far away from the surface,which is not conducive to the DET between Mv BOx and the surface.However,for GO surface,the interaction between Mv BOx and the surface is stronger,resulting in higher adsorption density,which further caused a higher catalytic current density on GO surface.In experiments,Mv BOx has the highest electron transfer rate on the RGO surface,but the strongest catalytic current density was found on the GO surface,these can be well explained at the molecular level by simulation results.3. The multiscale simulations,including PTMC and AAMD,have been performed to investigate the molecular adsorption mechanism?i.e.,adsorption orientation,conformation and effective DET?of Tc ACh E on charged surfaces?NH₂-SAM and COOH-SAM?.The effect of SCD on the adsorption were also studied.The simulation results indicate that when Tc ACh E adsorbed on positively charged surfaces,the active-site gorge orients toward the surface with the“end-on”orientation,the main negative potential patch adsorbs directly on the surface,and the active centre is close to the surface,which makes the path of the electron and enzyme substrate transfer shorter,and further induces a faster DET and more efficient reaction.On the contrary,Tc ACh E adsorbed on negatively charged surface with the“back-on”orientation.The main positive potential patch serve as the landing point of adsorption;the active-site gorge orients toward solution.Active residues are far away from the electrode surface,it is not good for the DET between enzyme and surface and the enzyme substrate transfer.The results indicate that the immobilization of Tc ACh E on positively charged surface is better for the Tc ACh E-based biofuel cells and amperometric biosensor.4. The adsorption mechanism of Tc ACh E on the amino-functionalized carbon nanotube?CNT-NH₂?,carboxyl-functionalized carbon nanotube?CNT-COOH?and pristine CNT surfaces were studied by PTMC and AAMD simulations.Simulation results shown that the active center of Tc ACh E orients and approaches the surface,and the active site gorge also orients and close to the surface when adsorbed on the positively charged CNT-NH₂,which is beneficial to the DET between the active center of the enzyme and the electrode surface,as well as the enzyme substrate transfer,which could improve the DET rate between Tc ACh E and the electrode surface.On the CNT-COOH and CNT surfaces,the active center and active site channel of Tc ACh E are oriented toward solution and far away from the surface,which is not conducive to DET and enzyme substrate transport.Furthermore,CNT-NH₂ surface can reduce the cost of enzyme substrate channel of Tc ACh E and the transfer path of enzyme substrate,accelerate the transfer rate of enzyme substrate to active center,and also accelerate the enzymatic bio-catalysis of Tc ACh E.The results indicated that the positively charged modified CNT-NH₂ surface is more suitable for the immobilization of Tc ACh E and can provide a better microenvironment for Tc ACh E biosensors.This dissertation sheds light on the orientation and conformation of Mv BOx and Tc ACh E adsorbed on the different functionalized nanomaterial surfaces at the atomistic level.The immobilization of Mv BOx and Tc ACh E on the nanomaterials interface by regulating the charged properties of the surface can be more fully utilized in their biocatalytic activity.It can provide practical theoretical guidance for the orderly immobilization of Mv BOx and Tc ACh E and the design,development,and improvement of the Mv BOx-based biofuel cells,Mv BOx-based biosensors and the Tc ACh E-based organic phosphorus pesticide biosensors.