Mesoscopic Coarse-Grained Simulations Of Lysozyme Interfacial Adsorption

Computer simulation has been an important tool in scientific researches. However, in the field of protein interfacial adsorption simulation, an appropriate coarse-grained simulation method between traditional atomistic and colloidal models is required. Due to the restriction of computing resource, the spatial scale and time scale of an atomistic simulation are very limited. In addition, the secondary structure and other native features of a protein are difficult to be effectively retained by colloidal model. Therefore, a mesoscopic coarse-grained simulation method based on the BMW-MARTINI force field has been used for protein adsorption in this work, which is suitable to explore the protein interfacial adsorption behavior at a greater spatial scale and longer time scale. Meanwhile, we also have carried out a series of validations and applications for this method. The major contributions of this dissertation are as follows:1. Mesoscopic coarse-grained simulations are adopted to study the adsorption behavior of lysozyme on different(hydrophobic, neutral hydrophilic, zwitterionic, negatively charged and positively charged) surfaces at the mesoscopic microsecond timescale. Simulation results indicate that:(i) the conformation change of lysozyme on the hydrophobic surface is bigger than any other studied surfaces;(ii) the active sites of lysozyme are faced to the hydrophobic surface, while they are exposed to liquid phase on hydrophilic surface;(iii) neutral hydrophilic surface can induce the reversible adsorption of lysozyme, while the nonspecific protein adsorption can be resisted by zwitterionic surface;(iv) when the ionic strength is low, lysozyme can anchor on the negatively charged surface easily, but can not adsorb on the positively charged surface; however, when ionic strength is high, a counter-ion layer is formed above the positively charged surface, which is the key factor why the positively charged lysozyme can also adsorb on the like-charged surface;(v) the major positive potential center of lysozyme, especially the residue ARG128, plays a vital role in leading the adsorption of lysozyme on charged surfaces.2. Hydrophobic charge induction chromatography(HCIC) is a new type of mixed-mode chromatography by regulating p H, in which the hydrophobic attraction controls protein adsorption whereas the electrostatic repulsion regulates protein desorption. Mesoscopic coarse-grained simulations results indicate that:(i) lysozyme can be adsorbed mainly with “top end-on” and “bottom end-on” orientation on hydrophobic surfaces, dominated by the two hydrophobic regions located at both ends of lysozyme’s long axis.(ii) Elution from the “top end-on” orientation is more difficult than that from the “bottom end-on” orientation;(iii) a higher ligand density can get a faster adsorption rate and stronger adsorption.(iv) The effect of ligand density on the desorption is mainly determined by the distribution probability of the positively charged groups of ligands;(v) a higher ionic strength can lead to a wider orientation distribution, a stronger adsorption and a lower elution rate. We can understand the molecular level interfacial mechanisms of HCIC on the mesoscopic time scale(2.0 μs). Meanwhile, this work might provide an efficient way to optimize the operating conditions and designing novel ligands.3. Nanomaterial curvature can influence the stability of native conformation of protein immobilized on nanomaterials, while the relevant mechanisms induced by the surface curvature effect is still far from been completely understand. Adsorption of single lysozyme on different-sized silica nanoparticles(SNPs) has been simulated at microsecond timescale by using mesoscopic coarse-grained molecular dynamics method. Results indicate that:(i) An increase in NP size, which leads to a decrease in surface curvature, can stabilize a preferred orientation distribution. However, it also can result in a greater loss of lysozyme conformation;(ii) The hydration layer above SNPs plays a vital role in the adsorption process of lysozyme on different-sized SNPs;(iii) a higher ionic strength does not significantly affect the behavior of lysozyme on SNPs.4. Protein corona formed by proteins and nanomaterials, is leading to the rapid development of various beneficial applications, including biomedicine, biosensors, biocatalysis, biomineralization, etc. Here, the protein corona simulations that needs a large spatial scale, are been carried out by mesoscopic coarse-grained method. The effects of lysozyme amount and ionic strength on lysozyme corona on different-sized SNPs are investigated at mesoscopic microsecond timescale. Simulations results indicate that:(i) an increase in lysozyme concentration can be favorable for the conformation stability of adsorbed lysozyme on SNPs. Moreover, the formation of ring-like and dumbbell-like lysozyme aggregation can further reduce the loss of lysozyme native conformation;(ii) for a smaller SNP, the increase of lysozyme concentration has a greater effect on lysozyme adsorption orientation. The dumbbell-like lysozyme aggregation is unfavorable for the stability of lysozyme adsorption orientation; however, the ring-like lysozyme aggregation can promote the orientation stability;(iii) the increase of ionic strength, can reduce the loss of lysozyme conformation and accelerate the aggregation of lysozyme during their adsorption process on SNPs. Thus, the formation of lysozyme aggregation can be regulated by ionic strength.In general, this thesis presents an efficient method, which is 100 times faster than traditional all atom molecular dynamics simulation. Thus, it can be applied for simulating the complicated protein corona systems which need a greater spatial scale and longer time scale. In this thesis, we have not only indicated a series of immobilization or nonfouling mechanisms for protein adsorption on different physicochemical surfaces, but also systematically revealed the influences of various factors on the protein interfacial adsorption mechanisms, which can provide helpful guidance for emerging applications(e.g., nonfouling materials, bioseparation, biosensors, biofull cell, biocatalysis, biomineralization, biodiagnosis, biomedical, etc) at the molecular level.