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The Effect of Hydrophobic Mismatch and Rigidity of Protein on the Cluster Formation of Transmembrane Proteins in Biomembranes

Jafarinia, Hamid Reza | 2015

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  1. Type of Document: M.Sc. Thesis
  2. Language: Farsi
  3. Document No: 46922 (08)
  4. University: Sharif University of Technology
  5. Department: Mechanical Engineering
  6. Advisor(s): Ahmadiyan, Mohammad Taghi; Jalali, Mir Abbas; Khoshnood, Atefeh
  7. Abstract:
  8. Membrane proteins aggregation is a very important biological phenomenon in a variety of cell functions. It has been suggested that aggregation behavior of membrane proteins is influenced by the shape of the hydrophobic domain of the proteins, proteins hydrophobic mismatch and bilayer curvature. However, in this study by means of coarse grained membrane simulations it has been found that in thermal equilibrium, protein-protein interactions also depend on protein rigidity and structural strength. Based on simulation results, we have observed stable large clusters even in the absence of hydrophobic mismatch between lipids and proteins. Interestingly, our results also indicate that proteins with low structural strength aggregate to form two-dimensional large clusters. Proteins with high structural strength, by contrast, form one-dimensional structures. Considering different size of proteins with various length of hydrophobic part, our simulations show different kinds of aggregation behavior. But even in the presence of hydrophobic mismatch, flexibility of proteins plays a significant role on the shape and size of the clusters. In order to clarify the result lipid density around proteins with different structural rigidity have been determined and it was found that lipid distribution around proteins affects the interactions between proteins. To thoroughly investigate and quantify the effect of the rigidity of proteins on membrane-mediated interactions of membrane proteins, we have investigated the effect of protein rigidity on the diffusive mobility of the lipids, surface tension of the bilayer and the bilayer profile around the inclusions
  9. Keywords:
  10. Biological Membrane ; Protein Structural Rigidity ; Rigid Protein ; Semi-Flexible Protein ; Protein Cluster Shape ; Lipid Density ; Hydrophobic Mismatch

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