Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations - September 10-14, 2014, Istanbul, Turkey

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.

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