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Coarse Grained Modeling of F-BAR Protein Interaction with Lipid Membrane

Nikbin, Ehsan | 2016

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  1. Type of Document: M.Sc. Thesis
  2. Language: Farsi
  3. Document No: 49330 (04)
  4. University: Sharif University of Technology
  5. Department: Physics
  6. Advisor(s): Ejtehadi, Mohammad Reza; Seyyed Reihani, Nader
  7. Abstract:
  8. F-BAR protein is one of the Bin/Amphiphysin/Rvs (BAR) superfamily proteins which contributes in curvature generation and stabilization of lipid membranes. These proteins usualy form lattices on the membrane and can sculpt the membrane. In this project the interaction of F-BAR protein with a lipid membrane is modeled using coarse grained molecular dynamics approach. In order to describe the curvature generation and stabilization we would need an appropriate coarse grained model for the lipid membrane. In this project the proposed model for the membrane describes a membrane in liquid phase with a lateral diffusion in the lipid bilayer. Depth and width of the lipids potential is determined in such a way that the bending rigidity of lipid membrane would be ~20 k_B T. Bending rigidity of the membrane is determined using thermal fluctuation method and from force measurement of tubular membrane. Bending rigidity values computed from thermal fluctuation of tubular membrane and from force measurement of tube is 20.3 k_B T ±1.1 k_B T and 23.0 k_B T ±2.1 k_B T respectively which are in good agreement with each other. Interaction of a lattice of F-BAR proteins with planar membrane is also studied to find curvature generation mechanism of F-BAR proteins, and we showed that high curvatures in membrane are formed in a short time by increasing the protein-lipid interaction strength. Bending rigidity of the membrane covered with F-BAR proteins is also computed using tube force measurement and thermal fluctuation method. Values of 32 k_B T to 105 k_B T are computed for bending rigidity of membrane by varying the protein-lipid interaction strength. We also showed that F-BAR proteins affinity is lower to curvatures higher than its own intrinsic curvature
  9. Keywords:
  10. Coarse Grain Molecular Dynamic ; Bending Stiffness ; Rigidity ; Lipid Membrane ; Bin/Amphiphysin/RVS (F-BAR)Protein ; Vesicle Curvature

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