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- Type of Document: M.Sc. Thesis
- Language: Farsi
- Document No: 44473 (04)
- University: Sharif University of Technology
- Department: Physics
- Advisor(s): Jalali, Mir Abbas; Ejtehadi, Mohammad Reza
- Abstract:
- Aggregation of membrane proteins plays a determinative role in many biological processes، such as signal transduction, cell division and endocytosis. In the present study, we have investigated the interaction between proteins in vesicles by means of coarse-grained molecular dynamics simulations. In the first step, a number of periodic lipid bilayers were simulated and their physical properties were calculated. Then, bilayers were immersed in water and converted into spherical vesicles via a selforganizing process . Finally two proteins were embedded into the vesicle and the potential of mean force (PMF) respect to the angle between them was obtained using umbrella sampling. This process was repeated for two vesicles with different radii. The resulting curves for the PMF show that the protein interactions are governed by tow factors: a repulsive depletion force and a long-range membrane-mediated force. These long-range interactions are due to the local deformation of the membrane. Comparing the PMFs obtained from vesicles with different radii reveals that the longrange interaction between proteins is stronger in the vesicle with larger radii. As a general trend, the long-range interaction of proteins depends on the curvature of the membrane surrounding them.Moreover, our simulations show that the curvature of the membrane influences the depletion force between proteins
- Keywords:
- Membrane Protein Aggregation ; Mean Force Potential ; Umbrella Sampling ; Biological Membrane ; Lipid Bilayer Membrane
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