Molecular Simulations Of Protein Adsorption On Self-assembled Monolayers

Protein adsorption on surfaces plays an important role in many biological processes. The behavior of proteins adsorbed on solid surface can be classified into two categories, specific adsorption and non-specific adsorption. In this dissertation, the interactions between protein and self-aeembled monolyers(SAMs)were studied by a multiscale approach, including parallel tempering Monte Carlo, all-atom molecular dynamics and coarse-grained molecular dynamics simulations. The effects of surface charge density and ionic strength on the orientation and conformation changes of protein on charged surfaces were investigated. Furthermore, the non-fouling mechanism of mixed-charged surfaces was also illustrated. The major contributions of this dissertation are as follows:1. The orientation of an antibody plays an important role in the development of immunosensors. Protein G is an antibody binding protein, which specifically targets the Fc fragment of an antibody. The orientation of prototypical and mutated protein G B1 adsorbed on positively and negatively charged SAMs was studied by parallel tempering Monte Carlo and all-atom molecular dynamics simulations. Simulation results show that with the same orientation trends, the mutant exhibits narrower orientation distributions than the prototype does, which was mainly caused by the stronger dipole of the mutant. Both kind of proteins adsorbed on charged surfaces were induced by the competition of electrostatic interactions and vd W interactions; the electrostatic interactions energy dominated the adsorption behavior. The protein adsorption was also largely affected by the distribution of charged residues within the proteins. Thus, the prototype could adsorb on negatively-charged surface, although it kept the net charged of-4 e. The mutant has imperfect opposite orientation when it adsorbed on oppositely charged-surfaces. For mutant on carboxyl-functionalized SAM(COOH-SAM), the orientation was the same as that inferred by experiments. While for the mutant on amine-functionalized SAM(NH2-SAM), the orientation was induced by the competition between attractive interactions(led by ASP406 and GLU5) and repulsive interactions(led by LYS10); thus, the perfect opposite orientation could not be obtained. On both surfaces, the adsorbed protein could retain its native conformation. The desired orientation of protein G B1, which would increase the efficiency of binding antibodies, could be obtained on a negatively-charged surface adsorbed with the prototype.2. Ribonuclease A(RNase A) adsorbed on oppositely charged surfaces with opposite orientations. The active site of RNase A is oriented toward the surface when it adsorbs on a negatively-charged surface; while for RNase A adsorbed on a positively-charged surface, the active site is oriented toward the solution. Negatively-charged surfaces could be used for RNase A removal since the catalytic active site is blocked. To bring the enzymatic catalysis of RNase A into play, positively-charged surfaces can be used to control the orientation of RNase A with the active site accessible. The dipole moment and side chains of RNase A on both surfaces are slightly changed, whereas the backbone structure of RNase A is well preserved. That is to say, RNase A preserves its native conformation during the adsorption process.3. The surrounding conditions, such as surface charge density and ionic strength, play an important role in enzyme adsorption. The adsorption of a non-modular type-A feruloyl esterase from Aspergillus niger(An Fae A) on charged surfaces was investigated by parallel tempering Monte Carlo and all-atom molecular dynamics simulations at different surface charge densities(±0.05 C·m-2 and ±0.16 C·m-2) and ionic strengths(0.007 M and 0.154 M). The adsorption energy, orientation and conformation changes were analyzed. Simulation results show that whether An Fae A can adsorb onto a charged surface is mainly controlled by electrostatic interactions between An Fae A and the charged surface. The electrostatic interactions between An Fae A and charged surfaces are weakened when ionic strength increases. The positively-charged surface at low surface charge density and high ionic strength condition can maximize the utilization of the immobilized An Fae A. The counter ion layer plays a key role in the adsorption of An Fae A on the negatively-charged COOH-SAM. The native conformation of An Fae A is well preserved under all these conditions.4. The orientation control of laccase on electrode is crucial for the direct electron transfer(DET) achieving. It is important to shorten the distance between the Cu T1 copper of laccase and substrate during the laccase immobilization. The orientation of T. versicolor laccase(Tv L) on oppositely charged SAM(i.e., NH2-SAM and COOH-SAM) were studied. Results show that the positively-charged surface can control the Cu T1 site closer to the surface. Tv L adsorbed on positively-charged surface with ‘end-on’ orientation and on negatively-charged surface with ‘lying’ orientation. The interaction energy and orientation of Tv L on positively-charged surface is more stable than that on negatively-charged surface. Thus, the positively charged surface is more conducive to the immobilization of Tv L. The native bioactivities of Tv L are well preserved when it adsorbs on charged surfaces. The simulation results could be applied to provide useful information for the design and development of laccase-based electrodes.5. Understanding the mechanism of the antimicrobial and nonfouling properties of mixed charged materials is of great significance. The interactions between human gamma fibrinogen(γFg) and mixed carboxylic methyl ether-terminated(COOCH3-) and trmethylamino-terminated(N(CH3)3+-) SAMs and the influence of hydrolysis were studied by molecular dynamics simulations. The two different thiols were mixed with the ratio of 1:1. After hydrolysis, the mixed SAMs exhibit behaviors from antimicrobial to nonfouling, since the COOCH3- thiols were translated to carboxylic acid(COO--) terminated thiols, which carried a net charge of-1 e. The adsorption and desorption behaviors of γFg on mixed SAMs and the water layer above the SAMs were also analyzed. Simulation results showed that the main differences between COOCH3-/N(CH3)3+- SAM and COO-- /N(CH3)3+- SAM are the charged property and the hydration layer above the surface. γFg could stably adsorb on the positively-charged COOCH3-/N(CH3)3+- SAMs. The adsorption behavior is mainly induced by the strong electrostatic attraction. There was a single hydration layer bound to the surface, which is related to the N(CH3)3+ groups. The van der Waals repulsion between γFg and the single hydration layer was not strong enough to compensate the strong electrostatic attraction. After hydrolyzation, the positively-charged SAM was transferred to a mixed-charged surface, the electrostatic attraction between γFg and the surface disappeared. Meanwhile, the SAM surface was covered by a ‘double hydration layers’, which was induced by the N(CH3)3+ and COO- groups. With the combined contribution of the ‘double hydration layers’ and the vanishing of electrostatic attraction, the γFg was forced to desorb from the surface. After hydrolyzation, the internal structure of SAMs looks more ordered due to the electrostatic interactions between charged groups on the top of SAMs.