Molecular Dynamics Simulation Of Peptide Amphiphilic Molecules By Self-assembly

Supramolecular material is a new functional material formed through self-assembly driven by non-covalent interactions.Peptide amphiphiles(PAs)are aggregated by the hydrophobic interaction of long chain alkanes,and the hydrogen bonds and electrostatic interactions function as the main driving force to achieve ordered self-assembly.Such materials are widely used in fields such as optoelectronic materials,bone healing,biomedical materials,biosensors and so on.In addition,cylindrical nanofibers with high aspect ratios can be obtained by changing external conditions such as light,pH,ions and enzymes.Due to its low toxicity and environmental friendly property,much concern has been attracted in a variety of industries including food,pharmaceutical and personal care.Molecular dynamics(MD)simulation can be introduced to learn about the probability of residues to form secondary structure and molecular information within the aggregates.In the third chapter,the interactions between amino acid surfactants of C12 Sar,C12Gly,C12 Ala,C12Mal,C12 Asp and C12 Glu were studied by MD simulation respectively The major factor determining the surface area of ??each head moiety was the ability to form hydrogen bonds between surfactants,indicating that the active agents were tightly packed together leading to weaker ability of forming hydrogen bonds with other molecules.With the addition of divalent counterions,the binding capacity of the surfactant molecules to the counterions increased,resulting in a more rigid conformation of the surfactant.In order to explore the aggregation and internal structures of amyloid protein(A?)in Alzheimer's disease,the amphiphilic molecules of C12-A?(11-17),C12-A?(16-22),C12-35)and C12-A?(37-42)were simulated.The fourth chapterintroduced the MD simulation of each slice of C12-A?(11-17)based on the corresponding experiment.At pH 3,with the increase of concentration,the conformation of the aggregates changed from micelles to single nanofibers and finally a plurality of nanofibers was formed.When a single layer of nanofiber was formed,the single nanofiber exhibited a certain helical structure with adiameter around 4.7nm,whichwas consistent with the experimental result.Hydrogen bond and hydrophobic surface area were analyzed in relation to the formation of aggregates.The fifth chapter discussed different aggregates formed by C12-A?(11-17),C12-A?(16-22),C12-A?(25-35)and C12-A?(37-42)at different pH values.The results show that the stable structure of C12-A?(11-17)is the nanofibers with chiral structure.The diameter of the nanofibers was basically the same with the experimental ones.The nanofiber with ?-sheet formed at PH7 was consistent with experimental hypothesis,and micelles were formed at pH11 and pH5.C12-A?(16-22),C12-A?(25-35)and C12-A?(37-42)can form nanofibrous structures under different pH conditions.When the head of the PAs molecules were electronically charged,the system cannot maintain the cylindrical structure due to the electrostatic repulsion in the system.Although the first residue was uncharged,the repulsion in the middle and the electrostatic attraction at the terminal caused the twisted nanofiber structure.If the head/terminal residues carried opposite charges,PAs would aggregate into a flattened structure,while same charge at the head and terminal of residues led to micellar structures.However,when residues adjacent to the ends had opposite charges at the terminal,the micelles can aggregate together.In summary,MD simulation shows that the structure of PAs nanofibers are affected by the polypeptide chain length,ion,concentration,and the location of the internal charge in the positive and negative forms.