Biology Reference
In-Depth Information
CHAPTER
Planning and Interpretation 23
Julia T. Philip, Aranda R. Duan, Emily O. Alberico and Holly V. Goodson
Department of Chemistry and Biochemistry, Interdisciplinary Center for the Study of
Biocomplexity, University of Notre Dame, Notre Dame, Indiana, USA
Using MTBindingSim as
a Tool for Experimental
CHAPTER OUTLINE
Introduction ............................................................................................................ 376
23.1 MTBindingSim ................................................................................................376
23.2 Experimental Designs in MTBindingSim............................................................376
23.3 Binding Models in MTBindingSim.....................................................................377
23.4 Using MTBindingSim Example 1: Tau-MT Binding.............................................379
23.5 Using MTBindingSim Example 2: Does Human EB1 Bind to the MT Seam
or Lattice? ......................................................................................................381
Conclusion ............................................................................................................. 383
References ............................................................................................................. 383
Abstract
MTBindingSim is a program that enables users to simulate experiments in which
proteins or other ligands (e.g., drugs) bind to microtubules or other polymers under
various binding models. The purpose of MTBindingSim is to help researchers and
students gain an intuitive understanding of binding behavior and design experiments
to distinguish between different binding mechanisms. MTBindingSim is open-
source, freely available software and can be found at bindingtutor.org/mtbindingsim.
This chapter first describes the capabilities of MTBindingSim, including the ex-
perimental designs and protein-binding models that it simulates, and then discusses
two examples in which MTBindingSim is utilized in an experimental context. In the
first, MTBindingSim is used to investigate potential explanations for unusual behav-
ior observed in the binding of the neuronal protein Tau to microtubules, demonstrat-
ing that some potential explanations are incompatible with the experimental data. In
the second example, MTBindingSim is used to design experiments to examine the
question of whether the plus-end tracking protein EB1 binds preferentially to the mi-
crotubule seam.
 
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