Author's School

School of Engineering & Applied Science

Author's Department/Program

Biomedical Engineering

Language

English (en)

Date of Award

5-24-2011

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Chair and Committee

David Sept

Abstract

The regulation of filamentous actin: F-actin) production from the polymerization of globular actin: G-actin) within the cell is critical for many cell functions. Since actin is found in all cells, understanding how actin-binding-proteins: ABPs) bind and how their regulating mechanisms work is not only important to the basics of cytoskeletal pathways, but also to understanding associated diseases and creating possible therapeutics to combat them. Cofilin is an ABP that plays an important part in the regulation process and in recent times, has come to be known as a player in maintaining a cell's homeostasis. It's activity has been shown to have implications in many diseases, such as Alzheimer's and certain cancers. Cofilin binds and severs actin filaments, leading to depolymerization as well as the creation of new barbed ends. Although some of the details of cofilin's interaction with G-actin have been illuminated through a range of experimental studies, the specific interactions with F-actin have remained much more elusive. As of yet, there are only cryoEM models of cofilin-bound F-actin: where the binding occurs at a 1:1 ratio), which are not high enough resolution and do not show molecular interactions. The focus of this research is to build a model of how cofilin binds F-actin and understand the mechanism of severing. Computational methods, such as protein-protein docking, all atom molecular dynamics: AA MD) simulations, and Coarse Grain MD: CG MD) can help in understanding the interactions between cofilin and F-actin. Iteratively combining these methods with biochemical and mutagenesis experiments to reach a consensus offer a guide towards a more cogent answer. Here in this dissertation, I describe how I built a cofilin and F-actin binding model, with the aid of empirical data. This work allowed me to create several filament models with varying number of bound cofilin, which replicates different binding states of the filament. I also simulated the dynamics of these filaments models to gain insight into filament behavior, particularly twist.

Comments

Permanent URL: http://dx.doi.org/10.7936/K7GT5K6G

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