ABSTRACT
Proteins are highly dynamic molecules exhibiting a complex conformational landscape modulated by their interaction with the solvent and dierent eectors. at conformational
CONTENTS 12.1 Allostery and Cooperativity in Proteins 223 12.2 Binding Polynomial in Intermolecular Interactions 226 12.3 Isothermal Titration Calorimetry: Characterizing Cooperative Interactions 234 12.4 Cooperative Homotropic Interactions: e Case of Nucleoplasmin Binding
Histones 235 12.5 Heterotropic Cooperative Interactions: e Case of β-Subunit From
F1-ATPase Binding Nucleotides 239 12.6 Concluding Remarks 244 Acknowledgments 244 References 244
landscape is constituted by an ensemble of states with populations or molar fractions dependent on their conformational Gibbs energy. e conformational Gibbs energy can be modulated by extrinsic factors such as temperature, pressure, pH, ionic strength, and ligands. Dierent conformational states of a protein interact with a given ligand with different binding anities, and thus the binding of the ligand will reduce their overall Gibbs energy to dierent extents. e conformational equilibrium is then redistributed toward those conformational states able to bind that ligand. In addition, the dierent conformational states possess dierent biological activities (i.e., dierent abilities to interact with other biological partners), and this phenomenon may lead to increased or decreased activity, or even to the acquisition of a new biological activity. erefore, the interaction of a protein with a ligand will determine its biological activity by inuencing its ability to interact with other ligands. us, in a broad sense, allosterism is the modulation of the protein conformational equilibrium by ligand binding (Wyman 1948, 1963, 1964; Wyman and Allen 1951; Del Sol et al. 2009). For example, as illustrated in Figure 12.1, if, in the absence of ligand A, a protein is able to interact with ligand B, but ligand A binding displaces the protein conformational equilibrium by populating a certain protein conformational state that does not interact (or show a very low binding anity) with ligand B, then the two ligands exhibit negative cooperativity; on the contrary, if ligand A binding displaces the protein conformational equilibrium by populating a certain protein conformational state that interacts better with ligand B, then the two ligands exhibit positive cooperativity. If ligands A and B are identical, it is called homotropic cooperativity; if ligands A and B are dierent, it is called heterotropic cooperativity. Although traditionally homotropic cooperativity has been directly associated with the oligomeric nature of proteins whose quaternary structure represents the structural and energetic basis for the cooperative eect, the fact is that many monomeric proteins display homotropic behavior (e.g., calmodulin, transferrin, and lectins).
