Adsorption And Transportation Behaviors Of Biomolecules On Nanomaterial Surfaces And In Nanopores

The interaction between biomolecules and solid surface is universal and complex in nature, and it is the fundamental issue in nanotechnology and biological technology, relating to the field of biomineralization, tissue engineering, biosensors and drug delivery and separation etc. For example, the adsorption of protein on hydroxyapatite (HAP) surface is the initial step of interaction between biomedical implants and tissue. The cells are recognized by adsorbed protein via surface acceptor and this process control the following biological responds. It is require the materials of biomedical implants (bone, teeth, skin, tissue etc) possess high protein adhesion ability, which ensure good biocompatibility and recovery of physiological function of biomaterials. So controlling the amount, orientation and conformation of adsorbed protein on biomaterial surfaces is the determine factor. In nanopores, biomolecules have different properties from bulk, for example, enhanced catalysis, enhanced stability of the native structure of proteins, new folding mechanisms of proteins, the ordered water structure etc. These novel discoveries bring the nanopores materials like carbon nanotubes (CNTs) have potential application in the field of biomedical materials, drug delivery systems, fast gene sequencing and biosensors etc. Investigating the interaction between biomolecules and solid materials by quantum chemistry calculation and molecular simulation has exhibit great advantages and become powerful tool beyond experimental methods.In this thesis, the adsorption and desorption behavior of one module of fibronectin that containing the cell binding site on the hydrophilic hydroxyapatite (001) surface were investigated by molecular dynamics (MD) and steered molecular dynamics (SMD) simulations. The adsorbed site and driving force, as well as the effect to conformation of cell binding site were carefully discussed. In this basis, the adsorption dynamics of one sub-domain of human serum albumin (HAS) on hydrophobic single-walled carbon nanotubes with different diameters were studied. Our result reveals the induced conformational change of protein on hydrophobic surfaces. Then the hydrophilic CNT surfaces carrying different charges were constructed and the hydrophobic neutral CNT surface was taken as the reference. The adsorption behavior and dynamics of B chain of insulin peptide on these surfaces were investigated by MD simulations. The significant role of ordered water molecules in hydration shell was well interpreted. By three-dimensional potential energy surfaces scan using quantum chemistry calculation, the water molecules arrangement, the diffusion mechanism and diffusion pathway of water molecules in carbon nanotubes with different chirality were carefully discussed. In conclusion, the major contributions of this work are as follows:1. The different properties and behaviors of residues in the vicinity of hydroxyapatite surface cause the local rearrangements of protein and led to a partial loss of its secondary structure. The electrostatic energy was determined to be the driving force of the interaction between the model protein and the HAP surface. In these simulations, the charged-COO?and-NH3+groups exhibit the strongest interactions with the surface. The conformations of the RGD loop, which relates to the cell adhesion activity, exhibit large discrepancy in different starting orientations of the protein, and this may strongly affect the biological activity of the RGD loop.2. The conformation and orientation selection of protein was induced by the properties and the texture of surfaces, which is deduced from the interaction curve and trajectory. After overcoming various energy barriers of the system, one or more residues in the protein which have affinity to the surface could be readily adsorbed and drive the interaction curve to the next step. During the adsorption process, the secondary structure of a-helices in the model protein was slightly affected. However, the random coils connecting these a-helices were strongly affected and it might alter the tertiary structure of the protein. These conformational changes may highly affect the activity of protein.3. Water molecules play a significant role in the peptide adsorption on charged-CNT surfaces, especially the first hydration shell outside the CNT surfaces. Compared to the peptide adsorption on neutral surfaces, more ordered hydration shells outside the CNT prevent more compact adsorption of the peptide in charged-CNT systems. This shield effect leads to the smaller conformational change and weaker vdW interaction between the peptide and the CNT surfaces. However, due to the strong electrostatic interaction between peptide and charged-CNT surfaces, the total interaction between the peptide and the charged surfaces in charged-CNT systems are much stronger than that in neutral surface system, which implies a stronger binding of the peptide. The result of these simulations implies that by charging the nanotubes, it is possible to improve the binding strength of peptide/protein on CNT surface, as well as keeping the integrality of the peptide/protein conformation.4. The potential energy surfaces scan of water molecule inside armchair (14,14) and zigzag (24,0) CNTs indicates that the diffusion energy barrier of water molecules in armchair (14,14) CNT is much lower than that in zigzag (24,0) CNT. Our calculation also reveals that in armchair (14,14) CNT, water molecules diffuse along the cylindrical surface in a spiral path while the water molecules tend to move circlewise around the central axis in zigzag (24,0) CNT. These results indicate the possibility to adjust the diffusion behavior of molecules inside CNTs by molecular engineering approach, without changing the pore size.