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Johns Hopkins University
This dissertation sits at the intersection of mechanics and biology. Specifically, we devise mesoscopic mechanochemical models to study biofilaments, very ubiquitous cellular protein structures. Since they undergo functional bending, twisting, buckling and stretching motions, understanding the mechanical response of biofilaments is crucial for a correct description of the conformational states of these proteins. Our models contribute to the better understanding of the nonlinearities in the mechanical response of biofilaments to the environmental perturbations, without resorting to computationally costly full atomistic simulations. Two important filamentous structures coiled-coil and actin make up the main concentration of our work. Coiled coils are a rope-like protein motif formed by two or more alpha helices. The energetic of a coiled coil involves a competition between elastic deformation and hydrophobic interaction of residues of each helix. The model treats alpha helices as elastic rods where each rod interacts with another exclusively through beads representing the hydrophobic residues. We validate our model using steered molecular dynamics simulations and compare it with continuum thin rod model. We analyze the bending, buckling and twisting behavior of coiled coil molecules of various lengths and conclude that a coiled coil molecule cannot be fully characterized by a simple single-parameter mechanical model. The second filamentous biological structure we study is filamentous actin, F-actin, which is an important player in eukaryotic cellular processes including motility, morphogenesis, and mechanosensation. Actin monomer, G-actin, polymerizes to form F-actin. G-actin is an ATP hydrolase and at any time it is bound to either an ATP or ADP molecule. Mechanical and chemical properties of actin filaments are strongly coupled to each other through the bound nucleotide type. In our model of F-actin, each monomer is treated as a spherical particle with a bound molecule identity. The particles are connected by a set of springs with changing mechanical properties that depend on the bound molecule. Using this model, we study and explain the behavior of actin filaments under various external mechanical stimuli introduced by actin binding proteins. Finally, we discuss the coupling of monomer chemical state changes to the global mechanical response of actin.
Biofilaments, Mechanobiology, Computational