| Actin, a highly abundant cytoskeletal protein found in all eukaryotic cells, plays a key role in many of the motive functions of the cell. To a large extent, these functions rely on the cycling of actin between its monomeric (G-actin) and polymeric (F-actin) forms, a conversion that is regulated by a complex interplay between the nucleotide bound at the core of each actin molecule and the interactions of actin subunits with one another and with actin-binding proteins. This regulation couples three scales of dynamics – 1) the hydrolysis of the nucleotide and rearrangement of the nucleotide binding cleft, 2) the conformation of the subunit, and 3) the properties of the actin filament. Static crystal structure images and low resolution experimental data do not provide us with a clear understanding of the mechanisms by which these scales interact. Computational methods, which offer a bridge between theory and experiment, provide us with a way to analyze dynamics across all three of these scales, predict mechanisms of coupling between scales, and propose experimental ways in which to validate these hypotheses. In this thesis, we explore 3 different aspects of actin dynamics that involve coupling between scales using molecular dynamics simulations and coarse-grained analysis. Through increasingly detailed models of the actin subunit, we address the questions of a) how conformational changes associated with polymerization affect the hydrolysis of the nucleotide at the core of actin, b) how the conditions of sample preparation in different models of actin may affect the resulting structure, and how stable these structures are during simulation, and c) how the nucleotide affects the energetics of flattening (the conformational change associated with filament formation) in monomeric actin and the implications that this has for the nucleotide regulation of polymerization rates. |
