Substrate-Modulated Thermal Fluctuations Affect Long-Range Allosteric Signaling in Protein Homodimers: Exemplified in CAP

Abstract

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.

Role of Fluctuations in Ligand Binding Cooperativity of Membrane Receptors

“…We can compare our numerical results for N R ¼ 2 and no lateral fluctuation with an analytical model along the lines given in Ref. [6]. Approximating the influence of (symmetric) ligand binding by an additional harmonic coupling k c , the system is effectively a system of coupled harmonic oscillators.…”

“…As proteins are flexible molecules, the allosteric signaling process might also depend on a change in conformational fluctuations [3]. Such a possibility has been explored for DNA binding proteins [4][5][6]. In addition to experimental evidence that supports a more dynamical mechanism of GPCRs [7], molecular dynamics (MD) simulations have ruled out previously proposed static mechanisms that consider only conformational changes [8].…”

“…Cooperativity in binding is defined as the difference between the sum of the standard free energy differences of the substeps (binding to one ligand only) and the standard free energy difference between reactions and products [11,12] (also known as the allosteric free energy ÁÁG [3,4,6]…”

Terahertz optical measurements of correlated motions with possible allosteric function

“…The minimum still is at the origin; that is, the minimum energy configuration does not change. This situation would be analogous to the allosteric interactions without any net conformational change with agonist binding, such as in the case of dimeric catabolite activator protein (McLeish et al 2013;Rodgers et al 2013;Toncrova and McLeish 2010). However the x-y coupling distorts the energy surface, and the eigenvectors now connect the minimum energy configuration to the target configuration.…”

Allosteric Activation via Kinetic Control: Potassium Accelerates a Conformational Change in IMP Dehydrogenase

“…Recent treatments of allostery emphasize that proteins exist in conformational ensembles, but the underlying effector-induced shift in the distribution of conformations still applies (5–8). An alternative model, termed dynamic allostery, posits that an effector changes the distribution of sub-states within a single conformation, and an example of this phenomenon is also known (Figure 1B; (9–11)). These models presume that the conformational ensemble is at equilibrium; re-cast in the language of a chemical reaction coordinate, these models invoke changes in ground state conformations, and are therefore examples of thermodynamic control.…”