Alternative Title

Effect of rigid and and segmented cargo on dynein movement

Publication Date

2016-5

Document Type

Honors Thesis

Department

Computer Science

Keywords

Dynein, Computer simulation, DNA, Motor protein, Modeling, DNA origami, Motor ensemble, Segmented chassis, Rigidity of cargo, Step size, Dwell time

Abstract

Cytoplasmic dynein is a molecular motor responsible for intracellular cargo transport towards the cell center in eukaryotic cells. It walks on microtubules and often works in small ensembles. Yet, many of the biophysical mechanisms that drive the interactions between dynein motors within ensembles are unknown. To examine the properties of dynein ensemble motility, previous studies used DNA origami techniques to create a rigid cargo "chassis." The chassis can have different numbers of motors attached in various geometries. In that study, we observed negative interference between motors and ensemble velocity decreased as the number of motors increased. Using a less rigid, segmented chassis, we observed ensemble velocity increased as the number of motors increased, suggesting that negative interference was reduced. Therefore, to better understand how cargo rigidity influences ensemble motility, we are developing a computational model of our dynein/DNA origami complexes. Every motor has a trajectory composed of step sizes and dwell times between individual steps. The trajectories are simulated dynamically based on the motors’ relative positions to each other. Various hypotheses regarding motor interactions, and thus the rules of when a motor can take a step, are tested.

Language

English

Comments

ix, 64 pages : color illustrations. Honors project, Smith College, 2016. Includes bibliographical references (pages 63-64)

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