Book of Abstracts: Albany 2009
June 16-20 2009
© Adenine Press (2008)
Allosteric Mechanism of Hexameric E. coli Arginine Repressor
Molecular dynamics simulations with ArgRC, the ~50 kDa C-terminal hexamerization and L-arginine-binding domain of E. coli arginine repressor, reveal the protein?s range of motions with and without bound L-arg. Simulations starting from the nearly identical apo- and holo-ArgRC X-ray crystal structures evolve distinctly during 20 ns. The two trimers of apoArgRC rotate freely with respect to one another between two limiting ensembles, one essentially like the starting state derived from the crystal structure and the other rotated in one direction by a mean of ~13 degrees. Simulations with holoArgRC having six L-arg ligands bound reveal essentially no rotational motion. The crystal-like ensemble of apoArgRC states is visited much less frequently than the rotated ensemble, consistent with bond occupancies and entropies in the two ensembles that likewise imply the crystal traps a high-energy state. Detailed analysis of the trajectories reveals that the motion of apoArgRC is unidirectional because the single arginine residue of each polypeptide chain faces one side of the L-arg-binding pocket and extends its sidechain into the pocket, mimicking the ligand. Simulations with the apoArgRC hexamer after adding six L-arg ligands confirm that, as in holoArgRC, rotational dynamics are suppressed and the most populated states are more crystal-like. Simulations with incremental additions of individual L-arg ligands reveal that a single bound L-arg is sufficient to suppress rotation and favor a more crystal-like ensemble. The proposed mechanism is corroborated by recent crystals of Mycobacterium tuberculosis ArgR, which present an arginine sidechain on the opposite side of the pocket and which trap a state that is rotated in the opposite direction. The results enable structure-based interpretation of the multiphasic thermodynamic profile of L-arg binding and predict its long-range structural consequences in intact ArgR.