Biology Reference
In-Depth Information
INTRODUCTION
Microtubules (MTs) are a protein-polymer that are a fundamental part of the cell
cytoskeleton and are involved in many critical cellular processes, such as cell divi-
sion, maintenance of cell polarity, and cargo transport (
Amos & Schlieper, 2005;
Desai & Mitchison, 1997; Howard & Hyman, 2003; Lansbergen & Akhmanova,
2006
). MTs interact with a vast, highly coordinated array of microtubule-associated
proteins (MAPs) to carry out these functions (
Lansbergen & Akhmanova, 2006
).
Researchers often investigate the interactions between MAPs and MTs by investigat-
ing their interactions
in vitro
. In particular, many MAP-MT interactions have been
probed using binding assays (e.g.,
Gupta et al., 2010, 2009; Zhu et al., 2009
), which
are powerful experimental tools often used in studies involving MTs. However, the
results of binding studies can be difficult to interpret in cases where the MAP-MT
interaction is not a simple 1:1 binding interaction with a single, well-defined
dissociation constant (
K
D
). To assist researchers in interpreting MAP-MT-binding
experiments,
Philip, Pence, and Goodson (2012)
have written a program to model
MAP-MT-binding interactions, MTBindingSim. MTBindingSim is also a useful
tool to help researchers train their intuition about MAP-MT binding and to aid in
the design of new experiments that would distinguish between different binding
mechanisms. While the text below focuses on using MTBindingSim to study inter-
actions between MAPs and MTs, some of the models used in MTBindingSim can be
used to simulate binding to any polymer, and still others are suitable for modeling
general protein-ligand interactions.
23.1
MTBindingSim
MTBindingSim simulates experimental data for various MAP-MT-binding mecha-
nisms (described below) according to user-specified values for the total MAP and
MT concentrations and the binding dissociation constant(s). MTBindingSim was
written in MATLAB and can be run either in MATLAB or as an independent pro-
gram that does not require MATLAB on Windows or Mac OS. MTBindingSim is
open-source software and the MATLAB code and independent programs are freely
available at bindingtutor.org/mtbindingsim. A user manual with detailed instructions
on the operation of MTBindingSim and the mathematical calculations used in sim-
ulating the binding curves is also available. Some text of this section has been
adapted from the user manual.
23.2
EXPERIMENTAL DESIGNS IN MTBindingSim
MTBindingSim can plot simulated curves from three different experimental designs.
The most common experimental method for investigating MAP-MT binding is a
cosedimentation assay, where MT polymer and MAPs are mixed in known quanti-
ties, incubated to allow the proteins to bind to equilibrium, and then centrifuged, which
