Molecular Dynamics Simulation of Actin: An Investigation into the Mechanical Properties

Mehrafrooz, Behzad | 2017

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  1. Type of Document: M.Sc. Thesis
  2. Language: Farsi
  3. Document No: 49591 (08)
  4. University: Sharif University of Technology
  5. Department: Mechanical Engineering
  6. Advisor(s): Shamloo, Amir; Firoozbakhsh, Keikhosrow
  7. Abstract:
  8. Actin is the most abundant protein in most eukaryotic cells. It is highly conserved and participates in more protein-protein interactions than any known protein. Actin plays a crucial role in cell motility, adhesion, morphology and intracellular transport. Its biologically active form is the filament (F-actin), which is assembled from monomeric G-actin. In this thesis, the mechanical properties and characteristics of both G- and F-actin are studied using molecular dynamics simulations. In general, this thesis can be categorized into two individual parts: First, steered molecular dynamics simulation was performed to assess tension of monomeric G-actin molecule, and stress-strain curves were obtained in aqueous solution, with either ATP or ADP bound in the nucleotide binding pocket. Moreover in this scope, a generalized model is proposed to extend the obtained result for the monomeric G-actin to the actin filament. Next, the mechanical properties of F-actin are investigated using both all-atom and coarse grained molecular dynamics simulations. The aforementioned mechanical properties include of young modulus, torsional and flexural rigidity and the viscoelastic modeling of F-actin. The comparison of the obtained result and literature reveals that molecular dynamics simulation serves as a precise and sufficient approach in nanomechanics modeling. The indings presented here may thus be a step towards a better understanding of the mechanical properties of actin that lead to multiscale modelings
  9. Keywords:
  10. Actin Filaments ; Mechanical Properties ; Cytoskeleton ; Molecular Dynamic Simulation ; Coarse Grain Molecular Dynamic ; Coarse Grained Model

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