Cooperativity
Cooperative binding are binding events in which the Binding Affinity of a molecule to an interaction partner is influenced by a preceding binding event. There are two kinds of cooperative binding.
Homotropic cooperativity means that the binding of molecule A to a molecule B increases or decreases the affinity of B for further molecules of A. The most well known example of homotropic cooperativity is oxygen binding to hemoglobin: after the first oxygen molecule is bound to one heme unit, the oxygen affinity of the other heme units increases to facilitate complete loading of hemoglobin with four oxygen molecules. Homotropic cooperativity comes with a non-1:1 binding stoichiometry, which can be analyzed using TRIC.
Heterotropic cooperativity on the other hand, refers to a change in affinity of the interaction of molecules A and B that is brought about by the binding of molecule C. An example for this is synaptotagmin- 1, a calcium sensor. It can bind both Ca 2+ and phosphatidylinositol 4,5- bisphosphate (PIP2). Binding of PIP2 to synaptotagmin- 1 increases the affinity of the sensor protein to Ca 2+. Heterotropic cooperativity in this example comes with a 1:1:1 stoichiometry, but other models (and more interaction partners) are possible. In GPCRs, heterotropic cooperativity between different binding sites is often referred to as allosteric modulation. To investigate heterotropic cooperativity, analyze the affinity of A to B in the presence of various concentrations of C.
Increasing affinity upon binding is called positive cooperativity, while a decreasing affinity is called negative cooperativity. When investigating interactions with TRIC that are known to exhibit homotropic cooperativity, use the Hill Model for fitting the binding curve. In all other, including unknown, cases, please use the Kd Fit Model.
Note that the Hill coefficient does not describe the stoichiometry of an interaction but rather it’s cooperativity. In general, when working with Hill coefficients results should be interpreted carefully.