Bulletin of the American Physical Society
2016 Annual Meeting of the APS Mid-Atlantic Section
Volume 61, Number 16
Saturday–Sunday, October 15–16, 2016; Newark, Delaware
Session C3: Biophysics and Medical Physics I |
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Chair: Qi Lu, Delaware State University Room: Sharp Laboratory 131 |
Saturday, October 15, 2016 2:00PM - 2:36PM |
C3.00001: Computational studies of protein fibrils and their interactions with micelles Invited Speaker: Cristiano Dias The aggregation of proteins into amyloid-like fibrils is a ubiquitous process that arises for many amino acid sequences given the right template and conditions. While some naturally occurring fibrils contribute to the survival of living organisms, e.g., silk fibrils that are used by spiders to capture their prey, amyloid fibrils are responsible for plaque formation in tissues which is a hallmark of Alzheimer's disease. Thus, a detailed understanding of how proteins aggregate forming fibrils has important implications in biology and medicine. Here, I will present a toy model to show that mature fibrils exist in equilibrium with dissolved proteins in a solution. The existence of equilibrium enables thermodynamic quantities to be determined from temperature dependent studies. I will then present results from all-atom molecular dynamics simulations in which thermodynamic quantities related to the dissociation of a protein from a fibril have been computed. This study is enabling an understanding of the molecular mechanisms accounting for the stability of amyloid fibrils. Thermodynamic quantities are also being incorporated into a coarse-grained model of fibril growth. If time permits, I will discuss how this model is being used to study micelle deformation by amyloid fibrils. [Preview Abstract] |
Saturday, October 15, 2016 2:36PM - 2:48PM |
C3.00002: Tear Film Dynamics Around a Rigid Model Blob Christiaan Ketelaar, Richard Braun Tear film break up (TBU) can occur after imperfections in the lipid layer arise. The imperfections may cause elevated evaporation, which causes TBU for large enough spots and grooves and for fast enough evaporation. TBU also occurs near smaller features in the lipid layer. These are apparently blobs of lipids that do not spread and which are too small for the evaporative mechanism to account for the dynamics. We investigate the tear film dynamics near a model rigid blob with a fixed constant surfactant concentration. We develop the lubrication-type equations that govern the tear film thickness, surfactant concentration, and osmolarity in the tear film beneath and near the blob. We perform numerical simulations for the evolution of the tear film thickness and analyze how the size of the blob, as well as the surfactant properties and transport, affect tear film dynamics. The thinning induced by the blob is of the correct time scale to compare with in vivo observations, and close comparison with the experiments will be made. [Preview Abstract] |
Saturday, October 15, 2016 2:48PM - 3:00PM |
C3.00003: Governing Principles of Multiprotein Complex Formation on The Cell~Membranes: Insights from Theory and Reaction-Diffusion Simulation Osman N. Yogurtcu, Margaret E. Johnson A significant number of the cellular protein interaction networks, such as receptor-mediated signaling and vesicle trafficking pathways, includes reactions that involve membranes as a molecular assembly platform. Membranes both reduce the search space and induce a cooperative binding effect for stabilizing complexes with multiple membrane recruiter molecule binding sites. Mathematical models along with computer simulations provide insight into the dynamics of complex formation and help identify general principles that govern successful recruitment and assembly on membranes. Here, using a very efficient in-lab developed single-molecule scale stochastic simulation software, we show that the magnitude of complex formation enhancement has a simple functional form that applies whenever membrane recruiter concentrations are sufficiently high, and surprisingly, is independent of the protein binding strength. We propose that membrane localization works as a mechanism that ensures assembly only at specific times (after recruitment to surfaces) but does not precisely regulate the proteins involved since they benefit equally from surface restriction. This robust strategy is employed by adaptor proteins involved in clathrin-mediated endocytosis in both yeast and mammalian cells, where their relatively weak binding interactions with one another prevents protein coat assembly in solution, but transitions to a rapid assembly on the plasma membrane. [Preview Abstract] |
Saturday, October 15, 2016 3:00PM - 3:12PM |
C3.00004: Automated Identification of Cholesterol Interaction Sites on G-protein Coupled Receptors Eric Rouviere, Clement Arnarez, Edward Lyman G-protein coupled receptors (GPCRs) are transmembrane proteins responsible for transmitting signals from the extracellular region into the cytoplasm of the cell. It is known that cholesterol molecules present in the cell membrane affect the stability and the function of many GPCRs by interacting with the protein surface. Cholesterol, however, does not interact uniformly over the surface of the protein. Certain areas on the protein (that we report as interaction sites) are more favorable to cholesterol binding. The goal of this work is to develop a robust method to locate and analyze these interaction sites to guide experimental tests. To achieve this goal, we used a coarse-grained model (Martini) and molecular dynamic simulations of an Adenosine A$_{\mathrm{2a}}$ receptor (A2AR) in a lipid bilayer embedding cholesterol molecules to identify the key residues involved in the A2AR/cholesterol interactions. Our simulations show that cholesterol is most likely to bind in three distinct areas on the surface of the protein. We identify the most important residues for each of the three interaction sites and compare them to published experimental and simulation data. Based on these results, future paths for the development of the method are discussed. [Preview Abstract] |
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