90
Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery Poster Session I
37-POS
Board 37
Charting the Thermodynamic Landscape of Nucleotide Binding of the Universally
Conserved Molecular Switch, Elongation Factor Tu.
Dylan Girodat
, Katherine Gzyl, Evan Mercier, Hans-Joachim Wieden.
University of Lethbridge, Lethbridge, Canada.
Protein design currently can produce scaffold structures that have the ability to bind to a specific
ligand with a particular affinity. However, rational design of a protein with the ability to bind to
two very similar ligands with a specific affinity is still a challenge. In order for this to become a
routine process we have to improve our understanding of how the structure and dynamics of
proteins have evolved to achieve fine-tuning of affinities as well as specificity for ligand
selection. As a model system we have studied the universally conserved GTPase Elongation
Factor Tu (EF-Tu). EF-Tu has the capability to bind to both GTP and GDP. Surprisingly, EF-Tu
binds to GDP with a 40 fold higher affinity. This is unexpected, as the extra interactions between
EF-Tu and the additional phosphate group on GTP should favor the latter interaction.
Here we report using rapid kinetics approaches the thermodynamic parameters that govern
nucleotide binding for both GDP and GTP of EF-Tu. Interestingly EF-Tu has evolved in such a
way that GTP and GDP binding differ based on the energy barriers of dissociation and not
association. We also find that the EF-Tu•GDP complex is enthalpically favored while the EF-
Tu•GTP complex is entropically favored. To investigate the thermodynamic parameters further
we performed Molecular Dynamic simulations of EF-Tu bound to the respective nucleotide.
These simulations allowed us to identify the dynamic features of EF-Tu that are likely to give
rise to the reported thermodynamic parameters. We identify a hydrogen bonding network within
EF-Tu that stabilizes the GDP conformation where as differences in water coordination favor the
GTP conformation. Our findings provide for the first time the dynamic and thermodynamic
properties that govern EF-Tu’s nucleotide binding properties.
