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Protein-Nanoparticle Interactions

Moharamkhani, Halime | 2012

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  1. Type of Document: M.Sc. Thesis
  2. Language: Farsi
  3. Document No: 44005 (04)
  4. University: Sharif University of Technology
  5. Department: Physics
  6. Advisor(s): Ejtehadi, Mohammad Reza
  7. Abstract:
  8. In this thesis, proteinnanoparticle interactions have been studied using Molecular Dynamics simulation. sT fN, is the studied protein in this work. It is one of the most important proteins in the blood fluid. In this work, nanoparticle has been modeled as a surface; because the radius of gyration of sT fN is less than 3nm, so when it is near an enough big nanoparticle (100200 nm), nanoparticle seems as a surface from the view of protein. The surface of nanoparticle consists of sodium ions. Surface of nanoparticle, has been modeled using two types of surface:flat surface and nonflat surface. Protein interaction with surface, has been studied in two different initial orientations with respect to the surface. Orientation 1: when the protein is near the surface on its N C terminal face. Orientation 2: when the protein is near the surface on the oppositeface of N C terminal. The amino acids, that have critical role in the protein adsorption on surface, have been found. Asp102 and Glu279, amino acids with negative charged side chain and Cys329, that is an amino acid with neutral but polar side chain, in fact it is C-terminal of sT fN.All of these amino acids, are located in the flexible parts of protein structure. The root mean square deviations calculated for all systems, indicates that in flat surface systems, this quantity is more than of corresponding non flat surface. In systems with flat surfaces, total electric dipole magnitude, when protein is near surface on its NC terminal face, is more than the system that protein is near surface, on its opposite face of N C terminal. This result applies to systems with non flat surface too. All of Molecular Dynamics simulation steps, have been performed, using Molecular Dynamics simulation package, Gromacs
  9. Keywords:
  10. Proteins ; Molecular Dynamic Simulation ; Nanoparticles

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