Cooperativity of ligand binding as a function of monomer-dimer equilibrium parameters and acceptor concentration

Dimerization-based control of cooperativity

Cooperativity of ligand-receptor binding influences the input-output behavior of a biochemical system and thus is an important determinant of its physiological function. Canonically, such cooperativity is understood in terms of ligand-receptor binding affinity, where an initial binding event changes the affinity for subsequent binding events. Here, we demonstrate that dimerization-a simple yet pervasive signaling motif across biology-can have significant control over cooperativity and even dominate over the canonical mechanism. Through an exhaustive parameter sensitivity analysis of a general kinetic model for signal-mediated dimerization, we show that quantitative modulation of dimerization processes can reinforce, eliminate, and even reverse cooperativity imposed by the canonical allosteric ligand-receptor binding affinity mechanism. The favored accumulation of stoichiometrically asymmetric dimers (those with ligand-receptor stoichiometry of 1 : 2) is a major determinant of dimerization-based cooperativity control. However, simulations demonstrate that favoring accumulation of such stoichiometrically asymmetric dimers can either increase or decrease cooperativity, and thus the quantitative relationship between stoichiometrically asymmetric dimers and cooperativity is highly dependent on the parameter values of the particular system of interest. These results suggest that the dimerization motif provides a novel mechanism for both generating and quantitatively tuning cooperativity that, due to the ubiquity of dimerization motifs in biochemical systems, may play a major role in a host of biological functions. Thus, the canonical, allosteric view of cooperativity is incomplete without considering dimerization effects, which is of particular importance as dimerization is often a necessary feature of the allosteric mechanism.

NMR characterization of cooperativity: fast ligand binding coupled to slow protein dimerization

We describe a general approach for analysis of 2D NMR spectra to evaluate the cooperativity of ligand binding and protein dimerization in coupled systems.

Proton-linked dimerization of a retroviral capsid protein initiates capsid assembly

In mature retroviral particles, the capsid protein (CA) forms a shell encasing the viral replication complex. Human immunodeficiency virus (HIV) CA dimerizes in solution, through its C-terminal domain (CTD), and this interaction is important for capsid assembly. In contrast, other retroviral capsid proteins, including that of Rous sarcoma virus (RSV), do not dimerize with measurable affinity. Here we show, using X-ray crystallography and other biophysical methods, that acidification causes RSV CA to dimerize in a fashion analogous to HIV CA, and that this drives capsid assembly in vitro. A pair of aspartic acid residues, located within the CTD dimer interface, explains why dimerization is linked to proton binding. Our results show that despite overarching structural similarities, the intermolecular forces responsible for forming and stabilizing the retroviral capsid differ markedly across retroviral genera. Our data further suggest that proton binding may regulate RSV capsid assembly, or modulate stability of the assembled capsid.

Pyromellitamide Aggregates and Their Response to Anion Stimuli

The N,N',N'',N'''-1,2,4,5-tetra(ethylhexanoate) pyromellitamide is found to be capable of both intermolecular aggregation and binding to small anions. It is synthesized by aminolysis of pyromellitic anhydride with ethanolamine, followed by a reaction with hexanoyl chloride. The single-crystal X-ray structure of the pyromellitamide shows that it forms one-dimensional columnar stacks through an intermolecular hydrogen-bonding network. It also forms self-assembled gels in nonpolar solvents, presumably by a hydrogen-bonding network similar to the solid-state structure as shown by IR and XRD studies. Aggregation by intermolecular hydrogen bonding of the pyromellitamide is also observed by NMR and IR in solution. Fitting of NMR dilution data for pyromellitamide in d6-acetone to a cooperative aggregation model gave KE=232 M-1 and positive cooperativity of aggregation (rho=0.22). The pyromellitamide binds to a range of small anions with the binding strength decreasing in the order chloride>acetate>bromide>nitrate approximately iodide. The data indicate that the pyromellitamide binds two anions and that it displays negative cooperativity. The intermolecular aggregation of the pyromellitamide can also be altered using small anion stimuli; anion addition to preformed self-assembled pyromellitamide gels causes their collapse. The kinetics of anion-induced gel collapse are qualitatively correlated to the binding affinities of the same anions in solution. The cooperative anion binding properties and the sensitivity of the self-assembled gels formed by pyromellitamide toward anions could be useful in the development of sensors and switching/releasing devices.

Influence of ligand valency on ligand-influenced monomer-dimer equilibrium systems and biological control mechanisms

Two specific ligand-influenced monomer-dimer equilibrium systems are discussed. Each has a ligand-to-dimer subunit ratio of 0.5. Equilibrium characteristics of the system are described in terms of the effect of a bivalent ligand on both experimental and theoretical analysis. It is shown that Hill expressions need to be modified for multivalent ligand systems, and care is needed in equilibrium parameter determination. Some unique properties of these systems are retained, yet others are altered in the presence of a multivalent ligand. A suggestion as to the minimum amount of information needed to describe completely a ligand-influenced monomer-dimer system is given. The estrogen-receptor system is presented as an attractive biological model for both theoretical and experimental study of ligand-influenced polymerizing systems and their role in cellular control requirements.