Molecular Simulation Of Enzyme Immobilization Mechanism For Bioenergy

Under the background of the current "dual-carbon" strategy,using enzymes to catalyze and degrade biomass resources into biofuels is not only conducive to alleviating the crisis of fossil energy depletion,but also beneficial to environmental protection while obtaining economic benefits.Enzyme immobilization can overcome the inherent drawbacks of free enzymes,such as instability,difficulty in separation and repeated use of.However,due to the shallow knowledge of enzyme immobilization mechanism at the atomic level,it still remains challenging to flexibly regulate the orientation and conformation of the enzyme on the support surface to improve the catalytic activity of the immobilized enzyme.Aiming at the above key scientific problems,in this paper,multi-scale molecular simulation techniques,including parallel annealing Monte Carlo simulation(PTMC),prediction of protein preferred orientation on a surface(ProtPOS),molecular docking(Patchdock)and all-atom molecular dynamics(AAMD)simulations are combined to study the interaction mechanism between enzymes that related to bioenergy conversion and the support surfaces,which provides theoretical guidance for the rational design of efficient and stable enzymesupport composite catalysts.1.The adsorption behavior of methionine-rich Thermus thermophilus laccase(TtLac)on the amino-functionalized(NH2-CNT)and carboxyl-functionalized carbon nanotube(COOH-CNT)surfaces were studied by combining PTMC and AAMD simulations strategy.Simulation results reveal that the charged properties of CNT are critical to regulate the direct electron transfer(DET)process between TtLac and the CNT surfaces.In addition,the methionine-rich β-hairpin motif is the key binding site for TtLac binding onto the NH2-CNT surface.The secondary structure fluctuation of TtLac on the NH2-CNT surface is less than that on the COOH-CNT surface or in the bulk solution,which allows the native conformation of TtLac to be well preserved.2.The multi-scale simulations combined with PTMC and AAMD were performed to investigate the effect of Na+ and Ca2+ ions on the activation of myriococcum thermophilum cellobiose dehydrogenase(MtCDH)on oppositely-charged self-assembled monolayer(NH2SAM and COOH-SAM)surfaces with different surface charge densities(SCDs).The results showed that Ca2+ was stronger than Na+ in promoting the conformation of MtCDW switch from the open state to the closed state under the same conditions However,high ionic strength(IS)of Ca2+ renders the cytochrome(CYT)domain of MtCDH away from the NH2SAM with low SCD.In contrast,whatever the IS,the NH2-SAM surface with high SCD can not only enhance the CYT-surface interaction but also achieve a closed-state conformation due to a similar role of Ca2+.3.The interaction mechanism between β-glucosidase(BGL)and the ZIF-8 surface are explored by the ProtPOS algorithm combined with A AMD simulations.First,the T4 lysozyme was used as a model protein to verify the accuracy of the ProtPOS algorithm,and the adsorption orientation results were consistent with the experimental study.AAMD results indicate that BGL adsorbed on the ZIF-8 with a "back-on" orientation with its active site channel oriented towards the solution.The free-energy of the adsorption process showed that the adsorption process is driven by enthalpy.In addition,the electrostatic interaction between negatively charged residues on the surface of BGL and Zn2+on the surface of ZIF-8 is the dominant driving force for adsorption.The secondary structure of BGL is not affected despite the strong adsorption with the ZIF-8 surface.4.The combination of the Patchdock method and AAMD simulation was used to investigate the adsorption behavior of Candida antarctica lipase B(CalB)on cellulose nanocrystals(CNCs)and its derivatives surfaces.It was found that the methylation and sulfonation of CNCs could promote the conformational of CalB switch from the closed state to the open state.The lid opening degree of CalB increased with the increase of methylation substitution degree of CNCs surface.Most importantly,when CalB adsorbed on the sulfonated CNCs surface,the lid opened to the maximum extent as the lid and α10 helices have a negative correlation movement pattern towards the opposite direction.