Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms

Abstract

Allostery has come of age; the number, breadth and functional roles of documented protein allostery cases are rising quickly. Since all dynamic proteins are potentially allosteric and allostery plays crucial roles in all cellular pathways, sorting and classifying allosteric mechanisms in proteins should be extremely useful in understanding and predicting how the signals are regulated and transmitted through the dynamic multi-molecular cellular organizations. Classification organizes the complex information thereby unraveling relationships and patterns in molecular activation and repression. In signaling, current classification schemes consider classes of molecules according to their functions; for example, epinephrine and norepinephrine secreted by the central nervous system are classified as neurotransmitters. Other schemes would account for epinephrine when secreted by the adrenal medulla to be hormone-like. Yet, such classifications account for the global function of the molecule; not for the molecular mechanism of how the signal transmission initiates and how it is transmitted. Here we provide a unified view of allostery and the first classification framework. We expect that a classification scheme would assist in comprehension of allosteric mechanisms, in prediction of signaling on the molecular level, in better comprehension of pathways and regulation of the complex signals, in translating them to the cascading events, and in allosteric drug design. We further provide a range of examples illustrating mechanisms in protein allostery and their classification from the cellular functional standpoint.

Fig. 1. Simplified diagrams illustrating the scheme of classification of allosteric mechanisms. The scheme uses six descriptors to describe an allosteric reaction: (1) the type of perturbation event at the allosteric site; (2) the extent of conformational change at the substrate site; (3) the dominant thermodynamic factor; (4) the type of allosteric cooperativity; (5) the location of functional site (is it coincident with the substrate site?), and (6) the functional oligomeric state in action. To facilitate module design in the representation, the core of an allosteric monomer is represented by a triangle. Each triangle edge is occupied by one of three sites: the allosteric site, the substrate site, and the functional site. Fig. 1A depicts a typical allosteric case in which the perturbation by an effector binding at the allosteric site causes a minor conformational change at the substrate site. The shape changes from circle (Off state) to triangle (On state) via multiple propagation pathways. The absence of an attached module to the third edge of the core triangle indicates that in this case the substrate site is also the functional location of the monomeric protein. The positive binding cooperativity is implied in Fig. 1A since no substrate is attached in the Off state. This is an enthalpy-driven allosteric regulation in that the unfavorable substrate binding (Off state) becomes favorable (On state) due to an effector binding at the allosteric site (Fig. 1B). In this simplified modular scheme, a representation of a particular allosteric mechanism is just a combination of various stimuli at the allosteric site (depicted in Fig. 1C) and of conformational changes at the substrate site (illustrated in Fig. 1D). A stimulus is an event that directly influences protein function. The numbers in parentheses provide a visual guide corresponding to the six descriptors of the classification scheme.

Fig. 2. Two simplified diagrams to illustrate the allosteric mechanisms of the exchange of GTP to GDP in example 1 in the text. In Fig. 2A, an extracelluar ligand binding at the N-terminal domain of the receptor (the allosteric site) causes a conformational change at the GDP binding site (the substrate site) leading to the release of GDP. This is a hetero-oligomer system with negative binding cooperativity driven mainly by enthalpy. The empty GDP binding site then becomes an allosteric site for GTP binding in Fig. 2B. The GTP binding event causes the dissociation of trimeric G-protein from the seven-helix receptor. If we retain the classification scheme with the seven-helix receptor as the core protein, the substrate will be the entire trimetric G-protein and the allosteric site is located inside the substrate; however, if we view the G-protein as the core protein, then the GTP binding is a negative cooperative binding leading to dissociation of the substrate, now the seven-helix receptor.

Fig. 3. Simplified diagrams to illustrate the allosteric mechanism of dimerization in example 2. The EGF binding event causes a large-scale, domain-movement conformational change at the substrate site, which in turn facilitates the dimerization. The extracellular dimerization process leads to a contact between the two intracellular functional sites, the cytoplasmic kinase domains. This represents a homodimer system where the substrate site is not at the functional site.

Fig. 4. Simplified diagrams to illustrate the allosteric mechanisms of the pre-formed dimer in example 3. Effector binding at the allosteric sites causes a large-scale conformational change at the substrate site, which brings the two separated substrates (the two triangles) in close contact to each other. This is a concerted homodimer system: the two substrate sites become the functional site when they are in close contact.