Molecular Simulations Of The Controlled Protein Adsorption At The Solid-Liquid Interface

Protein adsorption at the solid-liquid interface has a wide range of applications in many fields of life sciences. Therefore, exploration on the general rules of protein interfacial adsorption is of significant importance in the design of medical materials with better biocompatibility, improving the efficiency and activity of the immobilized enzymes, the design of biosensors with better responsiveness, and design of antifouling materials with stronger ability in resisting protein adsorption. In this dissertation, the adsorption orientation and conformation of cytochrome c(Cyt-c) and hydrophobin(HFBI) on various surfaces were investigated by a combined parallel tempering Monte Carlo(PTMC) and molecular dynamics(MD) simulation approach. Meanwhile, the general rules of the effects of electric dipole, hydrophobic dipole, surface chemistry, surface charged density(SCD), ionic type and ionic strength(IS) on protein adsorption have been discussed. The major contents and key points of this dissertation are as follows:1. The adsorption orientation and conformation of Cyt-c on bare Au(111) surface were investigated by PTMC and MD simulations. Simulation results show that the most favorable binding mode of Cyt-c on bare gold agrees well with the results characterized by SEIRA spectroscopy. The adsorption is mainly contributed by the strong van der Waals interactions between the surface and residues that have long side chains, which leads to the helix A and Ω1 loop of Cyt-c being in contact with the surface and most of the α-helixes being nearly parallel to the surface. The native structure of Cyt-c is well preserved during the adsorption, and only the flexible Ω1 loop and the N-terminal show a relatively larger mobility. The hindrance of ET is ascribed to the confined rotation of the heme prosthetic group and the farther positioning of the central iron to the surface(about 12.9 ?).2. The adsorptions of Cyt-c on five different SAMs(i.e., CH3-SAM, OH-SAM, NH2-SAM, COOH-SAM and OSO3--SAM) were studied by combined PTMC and MD simulations. Simulation results show that Cyt-c binds to the CH3-SAM through the hydrophobic patch(especially Ile81) with a slight reorientation after it settles on the surface, while the adsorption on the OH-SAM is relatively weak. Cyt-c cannot stably bind to the 7% protonated NH2-SAM even at a relatively high ionic strength; while a higher SCD(25% protonated NH2-SAM) promotes its adsorption. The preferred adsorption orientations of Cyt-c on the negatively charged surfaces are very similar with the heme group being close to the surfaces and the longest α-helix nearly vertical to the surfaces, regardless of the surface chemistry and SCD. As the SCD increases, more counterions are attracted to the charged surfaces, forming distinct counterion layers. The secondary structure of Cyt-c is well-kept when adsorbed on all these SAMs. The deactivation of redox properties for Cyt-c adsorbed on the CH3-SAM and highly negatively charged surfaces is due to the confinement of heme reorientation and the farther positioning of the central iron to the surfaces. This work may provide some guidance for the design of Cyt-c-based biosensors and controlled enzyme immobilization.3. The adsorption of Cyt-c on the amino-terminated self-assembled monolayer(NH2-SAM) and the effect of chloride and phosphate ions on the adsorption were studied by MD simulations. The results reveal that Cyt-c could not stably adsorb onto the surface even at a relatively high ionic strength when chloride ions were added, while phosphate ions could promote its adsorption. At a low phosphate concentration, Cyt-c can adsorb on the NH2-SAM mainly with two opposite orientations. One is similar to that characterized in the experiments for Cyt-c adsorbed on the NH2-SAMs, in which the heme group points far away from the surface; another orientation is similar to that for Cyt-c adsorption on the carboxyl-terminated SAMs. In the latter case, phosphate ions form a distinct counterion layer near the surface and overcompensated the positive charge of the surface. Further analysis show that chloride ions have no significant tendency to aggregate near the NH2-SAM surface and cannot shield the electrostatic repulsion between Cyt-c and the surface, while the phosphate ions can easily adsorb onto the surface and bind specifically to certain lysine residues of Cyt-c, which mediate its adsorption. At a high phosphate concentration, the phosphate and sodium ions will aggregate to form clusters, which results in a random adsorption orientation.4. The adsorptions of HFBI on four different SAMs(i.e., CH3-SAM, OH-SAM, COOH-SAM, and NH2-SAM) were investigated by PTMC and MD simulations. Simulation results indicate that the orientation of HFBI adsorbed on neutral surfaces is dominated by a hydrophobic dipole. HFBI adsorbs on the hydrophobic CH3-SAM through its hydrophobic patch and adopts a nearly vertical hydrophobic dipole relative to the surface, while it is nearly horizontal when adsorbed on the hydrophilic OH-SAM. For charged SAM surfaces, HFBI adopts a nearly vertical electric dipole relative to the surface. HFBI has the narrowest orientation distribution on the CH3-SAM, and thus can form an ordered monolayer and reverse the wettability of the surface. For HFBI adsorption on charged SAMs, the adsorption strength weakens as the surface charge density increases. Compared with those on other SAMs, a larger area of the hydrophobic patch is exposed to the solution when HFBI adsorbs on the NH2-SAM. This leads to an increase of the hydrophobicity of the surface, which is consistent with the experimental results. The binding of HFBI to the CH3-SAM is mainly through hydrophobic interactions; while it is mediated through a hydration water layer near the surface for the OH-SAM. For the charged SAM surfaces, the adsorption is mainly induced by electrostatic interactions between the charged surfaces and the oppositely charged residues. The effect of hydrophobic dipole on protein adsorption onto hydrophobic surfaces is similar to that of electric dipole for charged surfaces. Therefore, hydrophobic dipole may be applied to predict the probable orientations of proteins adsorbed on hydrophobic surfaces.