105
Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery Poster Session II
50-POS
Board 3
Computational and Experimental Insights into the Protein-Protein Cooperativity and
Catalysis of the GTPase enzyme RhoA and Activating Protein Rho.GAP
Whitney F. Kellett
, Nigel G. Richards.
Indiana University Purdue University Indianapolis, Indianapolis, USA.
GTPase enzymes, which hydrolyze guanosine triphosphate (GTP) to guanosine diphosphate
(GDP) and inorganic phosphate (Pi), are involved in a large number of critical cellular processes
including proliferation. GTPase Activating Protein (GAP) is responsible for the regulation of
GTPase. GTPase proteins, when poorly regulated, can signal for uncontrolled cellular growth
and are indicated in oncogenesis [1]. The objective of this study is to marry X-ray
crystallography, solution NMR and computational methodologies to reveal catalytic and
dynamic properties of the GTPase protein RhoA bound to the regulating protein RhoA.GAP.
Using this computational model as well as experimental insight, we study both the transition
state specifically and in context of the full catalytic cycle, using Quantum Mechanics (QM) and
Mixed Quantum and Molecular Mechanics (QM/MM) methodologies. Additionally, we use
long-time scale MM simulations to model the protein-protein interface, and use docking
methodologies to score libraries of compounds suited for interfering with this interface.
These simulations provide evidence for a dissociative transition state, pairing well with NMR
data. We suggest that the MgF
3
- crystallographic additive is the best adduct to date to model the
transition states of these types of enzymatic phosphoryl transfer reactions. These simulations also
provide the first complete catalytic model of a GTPase based phosphoryl transfer mechanism.
We also have identified structural effects of binding the RhoA.GAP protein to RhoA, and have
preliminary results that this interface may be selectively "drug-able" based on initial compound
screening. This model could be further exploited to identify ways to dissociate the errant
GTPase:GAP complex by targeting the GTP binding site or even the protein-protein interface
itself.
