Browsing by Subject "lipid bilayers"
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Item Mimicking anhydrobiosis on solid supported lipid bilayers(Texas A&M University, 2007-09-17) Chapa, Vanessa AlyssThe studies presented in this thesis focus on the synthesis of air-stable solid supported lipid bilayers by anhydrobiotic mechanisms. Supported lipid bilayers (SLBs) serve as platforms that mimic cellular membrane surfaces in appearance and behavior. One of the most attractive aspects of the SLB is that it exhibits two-dimensional fluidity that allows for individual components to rearrange as they would in actual cellular membranes. The one thing that would allow the SLB to become an ideal biosensor is the ability to remain stable in the absence of bulk water. As it stands now, unprotected SLBs are unstable in the presence of air causing the membrane to rearrange and delaminate from the surface. Several biological organisms utilize the process of anhydrobiosis to persevere in severe dehydrated states. Anhydrobiosis occurs when organisms employ large amounts of sugars, particularly disaccharides, to protect their cell membranes. The sugars, often released as a stress response, protect the membrane by replacing the water around the lipid headgroups while also interacting with other sugars to form a glass atop the bilayer. One of the most successful anhydrobiotic sugars has been trehalose, although other sugars have been evaluated and are capable of protecting lipid bilayers minimally. The experimental section of this thesis involves the creation of SLBs that are examined with and without the presence of sugar molecules. Essentially, the SLB was created, exposed to sugar solutions, dried, and subsequently rehydrated. Successful experiments occurred when rehydrated bilayers exhibited little damage and were mobile and functional. In addition to trehalose, several other mono- and disaccharides were used as were glycolipids, lipids with sugar headgroups. Upon the completion of all experiments it was clear that trehalose afforded the most protection of all species tested and that glycolipids do not sufficiently protect the membrane during rehydration. Therefore, the addition of a sugar such as trehalose to an SLB could allow for the creation of an air-stable biosensor that would be both practical and require little maintenance.Item Molecular dynamics simulation of complex molecules at interfaces: dendritic surfactants in clay and amyloid peptides near lipid bilayers(2009-06-02) Han, KunwooWe apply a molecular dynamics (MD) simulation technique to complex molecules at interfaces. Partitioning of dendritic surfactants into clay gallery and Ab protein behavior near hydrated lipids are chosen for the purpose. Using a full atomistic model of dendritic surfactants, the confinement force profiles featuring oscillatory fashion at moderate layer separation of 10 to 25 ? were observed. Integration of the confinement forces led to free energy profiles, which, in turn, were used to determine the final morphology of the nanocomposite. From the free energy profiles, smaller and linear surfactants (G1 and G2L) are expected to intercalate into the clay comfortably, while larger surfactants (G2 and G3) are expected to form frustrated intercalated structures due to the location and depth of the free energy minima. This would agree with the previous observations. As primary steps to understand the Ab protein behavior under biological conditions, simulations of bulk water and hydrated lipids were performed and the results were compared with the literature. Hydrated lipids were simulated using a full atomistic model of lipids (dipalmitoylphosphatidylcholine) and water with a cvff force-field and it was found that structural properties such as the molecular head group area and membrane thickness were accurately produced with MD simulation. Systems of the protein Ab(1-42) in bulk water were simulated and some secondary structural change, with loss of part of the a-helical structure, occurred during the 1 ns of simulation time at 323K. The fragment Ab(31-42) with b-sheet conformation was also simulated in bulk water, and the extended b-sheet structure became a bent structure. Simulations of Ab(1- 42) or Ab(31-42) near lipid bilayers have been performed to investigate the structural property changes under biological conditions. The different nature of structural change was observed from the simulations of the protein or fragment in water and near lipid bilayers due to the different solvent environment. The protein has close contacts with the membrane surface. It was impossible to observe the conformational change to b-sheet and protein entrance into the lipid bilayer within 1 ns simulations.