Doctoral Dissertations

Date of Award

5-2024

Degree Type

Dissertation

Degree Name

Doctor of Philosophy

Major

Chemical Engineering

Major Professor

Steven M. Abel

Committee Members

Steven M. Abel, Belinda S. Akpa, Andreas Nebenfuhr, Eric T. Boder

Abstract

The actin cytoskeleton is crucial for cellular processes and proper organization in cells. Physical regulators like actin crosslinking proteins, molecular motors, and physical confinement significantly impact the organization of the actin cytoskeleton. Despite advances, much remains unknown about how these physical regulators affect actin organization. In this thesis, we employ coarse-grained computer simulations to investigate the effect of physical regulators on the dynamics and organization of semiflexible actin filaments. First, we explore the role of crosslinker properties and confinement shape on actin organization by varying the system shape, the number and type of crosslinking proteins, and the length of filaments. We observe various structures, such as isolated clusters of filaments, highly connected filament bundles, and networks of interconnected bundles with loops. Our findings indicate that crosslinker properties not only influence the initial network response but also impact subsequent relaxation dynamics. We characterize the bending energy of individual filaments, identifying highly unfavorable filament configurations that, in some cases, are difficult to relax. Next, we examine the interplay between organelle transport and actin organization. We find that cargo transport can lead to the segregation of filaments into polarity-sorted domains, separated by aggregated clusters of cargoes. Dynamics of filament segregation are enhanced by larger numbers of cargoes, increased motors per cargo, and longer filaments. Subsequently, we utilize simulations to benchmark and develop morphometric parameters for the image-based characterization of crosslinked actin filament networks. We find morphometric parameters effectively measure aspects of actin network density, ordering, direction, and bundling. We show that established measures of bundling can be unreliable indicators of bundling in highly bundled networks. Consequently, we propose a new measure of bundling that better captures bundling levels. Finally, we present results from a preliminary study of the combined effects of crosslinkers, motors, and confinement on the self-assembly and dynamics of actin networks. Simulations reveal that sufficiently high numbers of motors per cargo induce deformations in highly crosslinked filament bundles. The work presented in this thesis offers mechanistic insights into the underlying biophysics governing the organization and dynamics of actin networks in both cellular and synthetic environments.

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