Classification assists not only in organizing information but also in making sense of observations: what are the differences between plants and animals; invertebrates and vertebrates; between cold and warm blooded animals; between mammals, birds, reptiles, fish, and amphibians; between classes of protein structures; drugs; types of interactions and chemical reactions. Sorting objects into distinct categories organizes the information, revealing patterns and relationships, and consequently provides insight. While the importance of classification is clear, how to classify and into which categories is less obvious. Relevant questions are (i) which properties to use; (ii) is the range of available cases sufficient; (iii) should categories lumped together require splitting; (iv) if we had started from different (to be discovered) examples, would the classification scheme be similar? A relevant classification scheme should relate to function and eventually must correlate with quantities allowing automated classification based on a set of analytical or empirical components. With these caveats in mind, we believe that the increase in the number of observed allostery cases, their breadth, the recent insight into allostery types and mechanisms, and their impact on cellular functions permits a first step in a classification scheme, which we expect to assist in organization, comprehension and in allosteric drug discovery.
Here we provide a comprehensive description and a framework for classification of allosteric mechanisms with some examples abstracted from a range of cellular processes. This was made possible by first obtaining a unified mechanistic view of allostery. The classification is based on several properties: presence/absence of conformational change; cooperativity type; driving thermodynamic terms; whether the substrate binding site and the functional site coincide; and role of phosphorylation (if present). We observed numerous examples of disorder-to-order conformational change with the first binding event prepaying the entropy cost. These common allostery cases display positive cooperativity and are lumped into the same classification bin. At the same time, order-to-disorder cases entail high entropy cost and fall into the negative cooperativity with conformational change rubric.
Mutations were not treated here. Yet, mutations can lead to disease via
allosteric effects. Consider for example the seven-helix transmembrane receptor. According to Pollard et al
over 600 mutations in more than 30 receptors of this family have been linked to disease. If the mutations occur at the ligand or the trimeric G-protein binding sites (including binding site truncation events, as for example at the N-terminal) these are not allosteric mutations. On the other hand, mutations occurring elsewhere and affecting binding are allosteric events. Mutations can lead to effector unfavorable N-terminal conformations; under such circumstances, there is no conformational change of the intracellular loops, thus no activation of the trimeric G-protein, which will remain in the receptor-bound state. These mutations lead to loss of function. In contrast, mutations leading to a conformational change at the G-protein binding site constitutively activate the reaction regardless of whether a ligand is bound. Mutations in tyrosine kinases can lead to disease. If these mutations are away from the binding sites, similar allosteric mechanisms may operate.51
Eventually, a systematic compilation and organization of available allostery cases, encompassing a range of effectors and environments within the functional signaling transduction context would be invaluable. Allostery is the vehicle through which function is exerted. Classifying allosteric cases transforms phenomenological descriptions to molecular mechanisms. To cite two examples, consider the text-book description of a GTP to GDP exchange in the seven-helix receptors case:42
here a classification scheme clarifies how the function is performed in this step of the catalytic phosphorylation signaling cascade. Classification indicates that two allosteric steps are involved (; example 1) where a substrate site initially occupied by GDP becomes an allosteric site which, via
negative cooperativity leads to the dissociation of the substrate, now the seven-helix receptor. Classifying the receptor tyrosine kinase case (example 2) clarifies that the functional site differs from the substrate binding site, a key mechanistic component which was unclear before (). Text books describe series of events; not mechanisms
. They cite the event and its consequences
: a certain gene knock-out will lead to a certain loss of function. Yet, in disease our goal is to be able to trace back to a particular signaling check-point; to identify the source of the functional loss. Further, a disease-related mutation does not have to be in the substrate or the functional sites; but it may block signal propagation.
Classification has proven immensely important in science. Here we provide the first classification framework for allostery based on six properties; this implies that a change in any of the six properties would affect function. A key question is which property would affect it the most. Hence, if the mechanism involves dimerization (example 2; property 6, ) concentration and binding constants are crucial. If the substrate binding site differs from the functional site (example 3; property 5 ) a mutation in the functional site can abolish substrate binding. If there is a hinge bending conformational change (examples 2 and 3; property 2) a mutation altering its extent can lead to functional loss; this property relates to propagation pathways and to dominant thermodynamic factors (property 3); mutations affecting perturbation (property 1) can have a similar effect to allosteric cooperativity (property 4): no perturbation, no cooperativity. Additional descriptors would surely be incorporated as the range of cases broadens. Clearly, figuring out allosteric mechanisms is crucial for the comprehension of how function is performed in the cell. Using a classification scheme along the lines proposed here should complement text-book descriptions; it should assist in the understanding of how the function is performed on the single molecule level within the framework of its complex cellular environment.