Design Of Non-covalent Modification Molecules Based On The Low-dimensional Carbon Nanomaterials

The interaction of biological molecules and solid materials is the basic problem of nanotechnology,biomaterials, and biotechnology, which have used in many fields such as tissue engineering, artificialorgans, biomaterials, and biosensors. To understand how the biological molecular conformational andorientation changes are effected by the interaction between them deeply is contribute to explore the originof life preferably, to design the suitable biological functional materials, and to be used for the preventionand treatment of disease. As an important element of life, carbon (C) can form many low-dimensionalnano-materials, such as:0D fullerenes (C60),1D nanotubes,2D graphene, and3D graphite. Comparedwith inorganic nanomaterials, they have better biological compatibility. And they can make use of thesurface coated or adsorb bioactive molecules (such as: drugs, proteins, and nucleic acids) as an effectivedrug carrier used in medicines and medical treatment, etc. However the surface of carbon nanometermaterials is highly hydrophobic, pristine carbon nanometer materials are easy to aggregate and lead to thetoxicity in the organisms, so they can not be directly used as drug carrier. The main approach to solve thisproblem is both covalently or non-covalently functionalized CNTs to improve the dispersion in the body.The non-covalently functionalized CNTs are increasingly developed because it could preserve thehybridization state, the native structure, and the electrical and mechanical properties of the carbonnanometer materials. Especially the adsorption of biological molecules such as proteins or DNA onto thesurface of the carbon nanometer materials has gradually become the basis of carbon nanometer materialsused as drug carrier. This kind of carrier can take bioactive molecules into the cell directly, then throughcontrol the release of drugs or slow down the release of drugs to raise curative effectly. The progress can avoid the effect of the body immune system and the enzyme system and can solve the compatibility anddegradation of the bioactive molecules in the body effectively. To explore the interaction mechanism of thebioactive molecules and the surface of nanometer materials actively can be great significance for surfacemodification of nanometer materials and the application of high efficiency carrier. The adsorptionbehaviors of protein onto the surface of carbon nanometer material such as: atomic adsorption type, theinteraction between the key adsorption atoms and the surface of material, can apply the eperimentalmethods such as fluorescence spectrometry et.al. So far, many biomolecules have been found to beabsorbed onto the surface of carbon nanometer materials spontaneously from both computational andexperimental studies. In spite of these exciting observations on biomolecules absorbed onto the surface ofcarbon nanometer materials, the dynamic mechanisms of these adsorption processes at the molecular levelremain bsure, which limits the biological and biomedical applications of carbon nanometer materials. Tothis end, the molecular simulation shows a huge advantage to help ones to better understand the dynamicmechanism in the bio-nano-systems, and establish new concepts for controlling the performance of suchsystems to facilitate the design and optimization of CNT-based functional nanoscale devices.In this thesis, molecular dynamics (MD) simulation was performed to investigate the spontaneousadsorption of proteins/peptides onto the surface of carbon nanometer materials, as well as the atomicdetails of the interactions taking place at the molecular level, and the dynamic mechanisms of thebiomolecules-CNT systems.1. The insulin which is rich in-helix and the WW domain which is rich in-sheet were selected asthe model proteins to investigate the adsorption behavior and adsorption differences between them and thedifferent size-SWCNTs. And the key adsorption residues were screened out. Then based on the conclusionof the main attractive force was the VDW interaction between protein and SWCNT, two peptides composed of long alkyl residues only and aromatic residues only were constructed.2. There are twenty polypeptide molecules which composed of single amino acid were designed inthis thesis. The twenty peptides were put onto the surface of graphene to investigate the adsorptionbehavior、adsorption state、adsorption attractive force、adsorption strength, and the orientation ofadsorption residues between them, respectively. Then the various properties of the twenty peptides werecomparative studied and classified studied. It was found that acidic amino acids were hard to absorb ontothe surface of graphene while the basic, nonpolar, and polar amino acids were easier to interact withgraphene. And the adsorption state of peptides were influenced by itself structures bigger.3. The interaction mechanisms of the two model proteins on the surface of the graphene wereinvestigated. The adsorption differences of the peptides onto the SWCNTs and the graphene werecompared and the absorption of proteins onto the surfaces of difference curvature carbon nano-materialswas investiged. The orientation change of the various proteins, the absorption behavior, and absorptionmecheniam were studied deeply at the same time. It was found that the peptides are easier to spread out inthe flat structure of the graphene surface, and the VDW interaction force between peptides and graphenecould damage the secondary structure of the peptides; the key absorption residues were found along thecurvature of the surface of different carbon nano-materials; the curly structures in proteins/peptides wereeasy to absorbed onto the surface of carbon nano-materials; comparing to the secondary strucuture ofprotein, the proteins which have the complicated tertiary structure were influenced by strucutures moreeasily.