Effectors of Rab GTPases: Rab Binding Specificity and Their Role in Coordination of Rab Function and Localization - Ras Superfamily Small G Proteins: Biology and Mechanisms 2 - page 50

3.2.4 Rab Structural Plasticity Contributes to Effector
Binding Specificity

A comparison of the structure of uncomplexed GTP-bound Rab proteins and their
structure within the Rab:effector complex reveals two different binding modes for
Rab:effector interactions. Most of the Rab effectors show little or no conforma-
tional change upon binding to Rab proteins. This binding mechanism could be
characterized as key-lock mechanism. For example, comparison of the structures of
unbound Rab3 and Rab3 bound to Rabphilin-3 demonstrates that the Rab3 structure
is preformed for Rabphilin-3 recognition and binding (Ostermeier and Brunger
1999 ) (Fig. 3.5 ). In contrast, Rab11 exhibits a significant structural change upon
effector binding that is expressed in a conformational rearrangement in switch II
upon FIP2/3 binding (Eathiraj et al. 2006 ; Shiba et al. 2006 ; Lall et al. 2013 ) and is
even more pronounced in the MyoVb:Rab11 complex (Pylypenko et al. 2013 ). In
this complex, the conformation of both switches and of the hydrophobic triad
residues is changed in the Rab:effector structure in comparison to uncomplexed
Rab11:GTP. This demonstrates the importance of structural plasticity of Rab pro-
teins for binding of some effectors, and it indicates a possible induced-fit mecha-
nism of the binding. Of note, Rab6 binds to its effectors with different binding
modes. R6IP1 recognizes and binds Rab6 without a conformational change
(Recacha et al. 2009 ), whereas GCC185 binding requires remodeling of the hydro-
phobic triad residues that is also associated with a shift of switch II (Burguete
et al. 2008 ). These observations demonstrate that not only the amino acid compo-
sition but also their conformational flexibility contribute to Rab:effector binding
specificity.

3.3 Affinities of Rab Effector Interactions

The affinities between active Rab GTPases and their cognate effectors span a wide
range from 40 nM to 16 M (Table 3.3 ). Even though some interactions are of

moderately high affinity, the interaction between the molecules remains dynamic
on a physiologically relevant timescale. Likely, dynamic binding of effectors is
required to permit the efficient binding of GAPs at the end of the Rab cycle in order
to allow its enzymatic deactivation. Since effectors and GAPs share overlapping
binding sites on Rabs, dynamic binding ensures access of the GAP to the Rab due to
the rapid spontaneous dissociation of the effector. It could be already demonstrated
with the high-affinity binding protein LidA from Legionella pneumophila that a
high-affinity Rab binding protein (with a pico- to nanomolar K d ) can act as a
competitive inhibitor for GAP binding (Schoebel et al. 2011 ; Neunuebel
et al. 2012 ). This demonstrates that the dissociation rate of the effector protein
can largely influence the accessibility of the Rab protein for a GAP protein and can
therefore indirectly regulate the speed of deactivation. Especially in processes that

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