Assembly Of Amyloid Fragments Under The Action Of Carbon Nanotubes And Assembly Of Nanowater In An External Field

Recent experimental and therical studies show that Carbon nanotubes have certain biological characteristics and bionic properties. For example, carbon nanotubes (CNTs) impact the aggregation process of proteins associated with neurodegenerative diseases; CNTs can be regarded as the simplified models of Biological channels or ribosomal. Many studies on these aspects are published. However, the details of molecular interactions between proteins and carbon nanotubes are still not well understood. In this thesis, we investigate the initial adsorption features, conformation changes and dynamics of forming (3-barrels of the Alzheimer’ s amyloid-βpeptide spanning residues 25-35 (A(325-35) on a single-walled carbon nanotube (SWNT) surface using fully atomic molecular dynamics simulations (MD) in explicit solvent. In order to understand the mechanism of this sort of assembly, we investigate the forces to drive the assembly based on a simple model and ensemble theory. In addition, the structures of nano-water confined biological channel and ribosome also have important biological significance, which also received wide attention. In his thesis, the effects of electric field on the phase behaviors of water encapsulated in a thick single-walled carbon nanotube (SWCNT) (diameter=1.2 nm) have been studied. We found that liquid water confined in SWNT can freeze into new ice phase under electric field.The thesis consists of four parts. The first part is a brief introduction of the characters, importance and status of the protein and protein aggregation, and the structure and properties of carbon nanotubes. The second part included in the second chapter is the principles and the simulation methods by computers. The third part is the most important one of this thesis, which contains the third, fourth, and fifith chapter. At first, using molecular dynamics simulations, we studied the dynamic process of (3-barrel forming on the surface of carbon nanotubes. Secondly, the thermodynamic properties of macromolecules’self-assembly driven by the hydrophobic interaction are investigated based on the esemble theory. In addition, the phase transition behaviors of water confined in carbon nanotubes under external electric field are also studied. The summary of the thesis and prospect of the future research are given in the last part. The contents of each chapter are given as follow:In chapter 1, the introduction of the characters, importance and status of the protein are briefly describled. In chapter 2, a brief introduction of the simulation methods and the ensemble theory are given.In chapter 3, we have investigated the interactions of two Aβ25-35 oligomeric b-sheets with a SWNT and the dynamics process ofβ-barrel formation in explicit solvent. We find that Aβ25-35 b-barrel formation involves at least two steps:i), curving of the Aβ25-35 b-sheets as a result of strong hydrophobic interactions with carbon nanotube concomitantly with dehydration of the S WNT-peptide interface; andⅱ), intersheet backbone hydrogen bond formation with fluctuating intrasheet hydrogen bonds. Detailed analysis of the conversion shows that b-barrel formation on SWNT surface results from the interplay of dehydration and peptide-SWNT/peptide-peptide interactions. Implications of our results on amyloid fibril inhibition are discussed.In chapter 4, we investigate the thermodynamic properties of macromolecules’ self-assembly driven by the hydrophobic interaction based on the esemble theory. Also found is that entropy and enthalpy (from the hydrophobic interaction) can cooperate to drive self-assembled macromolecules.In chapter 5, we studied the phase transition behaviors of water confined in carbon nanotubes under external electric field. Some new ice phase are found in our simulations.In chapter 6, we give a summary and the expection of future research of the thesis.