Biology Reference
In-Depth Information
models are valid for any protein-polymer or ligand-polymer interaction. The
other models are valid for any protein-protein or ligand-protein interaction. The cal-
culations performed by MTBindingSim are based on the definitions of the dissoci-
ation constants and mass balances for each binding model. Detailed derivations of
the equations used in MTBindingSim can be found in the user manual available
at bindingtutor.org/mtbindingsim.
Binding ratio
: Some MAPs appear to interact with MTs at ratios differing from 1
MAP:1 tubulin dimer. MTBindingSim allows for such situations by including
the binding ratio,
n
, as a user-specified input. The binding ratio is defined as
n
*A:1 tubulin dimer in all models in MTBindingSim. MTBindingSim includes
n
in its calculations by setting the concentration of initial available binding sites to
the concentration of free polymerized tubulin dimers ([MT] free) and only taking
the binding ratio into account when calculating how many binding sites have been
occupied by a binding event.
First-order binding
(
Fig. 23.1
A): In this model, the MAP A binds to MTs in a 1
MAP:1 tubulin dimer fashion with a dissociation constant
K
AMT
. In this model, all
A-MT interactions are identical.
Seam and lattice binding
(
Fig. 23.1
B): In this model, A can bind to either the MT
seam (
lateral tubulin contacts, forming 1/13 of the number of tubulin dimers) or
the lattice (
a
-
a
and
b
-
b
lateral tubulin contacts, forming 12/13 of the tubulin dimers)
with dissociation constants
K
AS
and
K
AL
, respectively (heterogeneity of protofila-
ment numbers is not currently taken into account).
-
a
b
A
B
C
K
AMT
K
AL
K
AMT
K
AS
K
AAMT
K
AA
D
E
K
AMT
K
AA
K
AMT
K
AA
K
AA
FIGURE 23.1
Cartoons illustrating binding models from MTBindingSim. (A) First-order binding.
(B) Seam (1/13 of the MT polymer) and lattice (12/13 of the MT polymer) binding. (C) MAPs
dimerize, where a MAP can exist either as a monomer or as a dimer, each with different
affinities for the MT. (D) MAPs bind MT-bound MAPs, where the binding of a MAP to the MT
creates a new MAP-binding site. (E) Two MAPs bind MT-bound MAPs, where each MAP
bound to the MT surface can bind two more MAPs.