Dissecting a ligand into smaller fragments can provide a strategy for analyzing the role of key functional groups in a protein-ligand interaction. Conversely, low-affinity ligand fragments that are able to occupy a receptor-binding site simultaneously, can often be linked together to form high-affinity inhibitors. The key challenge to such studies lies in measuring the thermodynamics of low-affinity interactions. This white paper will address the issues of studying low-affinity systems by Isothermal Titration Calorimetry (ITC). Topics will include working with receptor concentrations below KD (i.e., low c-values), and how displacement techniques can be employed to measure very low affinities while still complying with the c-value rule. Illustrative examples will be drawn from studies with carbohydrate-binding proteins.
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