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Vibration Modes of Membrane Proteins by Application of Elastic Network Model

Besya, Azimberdy | 2011

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  1. Type of Document: Ph.D. Dissertation
  2. Language: Farsi
  3. Document No: 42214 (48)
  4. University: Sharif University of Technology
  5. Department: Institute for Nanoscience and Nanotechnology
  6. Advisor(s): Ejtehadi, Mohammad Reza; Mobasheri, Hamid; Naghdabadi, Reza
  7. Abstract:
  8. Outer membrane proteins play the role of molecular machines in the outer membrane of bacteria to regulate their basic functions. These macromolecules have nano-scale dimensions and they are involved in the classifications of nano-machines and nano-pores. Protein structure is constructed of chain of amino acids. Coarse grained elastic network model of the protein introduces a network of selected point masses, which is located on α-carbon of each amino acid, linked together with harmonic springs that represent the interactions between residues, both the chemical (protein backbone) and physical bonds. Using the harmonic network potential and theory of mechanical vibration, normal modes of vibration and natural frequencies are calculated. Debye-Waller temperature factor (B–factor), which is a measurable quantity by x-ray crystallography, is used as probes for verifying and improving computational model. The primary results show discrepancies between experimental and computational results. It is shown in this thesis that is because of disregarding membrane-protein interactions. To improve the computational model, we impose constraints to the outer portion of protein by connecting each node in the outer portion to a virtual stationary node on the protein central axis having the identical z coordinate. We observe that by using these constraint springs, where by a few orders of magnitude are significantly improved are softer than the springs connecting the rest of residues, results significantly are improved. Total entropy calculation of elastic network shows that the low frequency non-rigid normal modes have higher share of total entropy and consequently higher probability of occurrence. Using HOLE program, the pore size of membrane proteins are calculated and a mini-channel inside the OmpF protein is observed.

  9. Keywords:
  10. Nanopore ; Normal Mode ; Outer Membrane Protein ; Elastic Network Model ; B-Factor

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