The role of conformational dynamics in allosteric signaling of proteins is increasingly recognized as an important and subtle aspect of this ubiquitous phenomenon. Cooperative binding is commonly observed in proteins with twofold symmetry that bind two identical ligands. We construct a coarse-grained model of an allosteric coupled dimer and show how the signal can be propagated between the distant binding sites via change in slow global vibrational modes alone. We demonstrate that modulation on substrate binding of as few as 5-10 slow modes can give rise to cooperativity observed in biological systems and that the type of cooperativity is given by change of interaction between the two monomers upon ligand binding. To illustrate the application of the model, we apply it to a challenging test case: the catabolite activator protein (CAP). CAP displays negative cooperativity upon association with two identical ligands. The conformation of CAP is not affected by the binding, but its vibrational spectrum undergoes a strong modification. Intriguingly, the first binding enhances thermal fluctuations, yet the second quenches them. We show that this counterintuitive behavior is, in fact, necessary for an optimal anticooperative system, and captured within a well-defined region of the model's parameter space. From analyzing the experimental results, we conclude that fast local modes take an active part in the allostery of CAP, coupled to the more-global slow modes. By including them into the model, we elucidate the role of the modes on different timescales. We conclude that such dynamic control of allostery in homodimers may be a general phenomenon and that our model framework can be used for extended interpretation of thermodynamic parameters in other systems.

Changes in the structural dynamics of double stranded (ds)DNA upon ligand binding have been linked to the mechanism of allostery without conformational change, but direct experimental evidence remains elusive. To...

of the activation energy barrier, and Dx U, the distance to the transition state. For all protecting osmolytes we measure DG U increases, demonstrating that the I27 protein is stabilized. More striking is the measurement of Dx U . Unfolding the I27 protein in water gives a Dx U ¼ 2.5 Å , a distance similar to the size of a water molecule. Water molecules have been identified as integral components of the unfolding transition state of the I27 protein, forming a solvent bridge between two b-strands. By varying osmolyte molecule size we rigorous test this solvent bridging hypothesis. We find that Dx U correlates with osmolyte size for molecules ranging in size from 2.5 Å to 5.6 Å . However, for larger molecules (> 5.6 Å ) Dx U remains unchanged relative to the value measured in water, suggesting these osmolytes do not participate in solvent bridging in the transition state. These studies uniquely probe the length scales over which solvent molecules can modify the molecular architecture of the unfolding transition of a protein, an area which remains beyond the reach of other experimental techniques.