Allosteric regulation


In the fields of biochemistry and pharmacology an allosteric regulator is a substance that binds to a site on an enzyme or receptor distinct from the active site, resulting in a conformational change that alters the protein's activity, either enhancing or inhibiting its function. In contrast, substances that bind directly to an enzyme's active site or the binding site of the endogenous ligand of a receptor are called orthosteric regulators or modulators.
The site to which the effector binds is termed the allosteric site or regulatory site. Allosteric sites allow effectors to bind to the protein, often resulting in a conformational change and/or a change in protein dynamics. Effectors that enhance the protein's activity are referred to as allosteric activators, whereas those that decrease the protein's activity are called allosteric inhibitors.
Allosteric regulations are a natural example of control loops, such as feedback from downstream products or feedforward from upstream substrates. Long-range allostery is especially important in cell signaling. Allosteric regulation is also particularly important in the cell's ability to adjust enzyme activity.
The term allostery comes from the Ancient Greek allos, "other", and stereos, "solid ". This is in reference to the fact that the regulatory site of an allosteric protein is physically distinct from its active site. Allostery contrasts with substrate presentation which requires no conformational change for an enzyme's activation. The term orthostery comes from the Ancient Greek orthós meaning "straight", "upright", "right" or "correct".

Ortho vs. allosteric inhibitors

Orthosteric

  1. Binding Site: Orthosteric inhibitors bind directly to the enzyme's active site, where the substrate normally binds.
  2. Mechanism of Action: By occupying the active site, these inhibitors prevent the substrate from binding, thereby directly blocking the enzyme's catalytic activity.
  3. Competitive Inhibition: Most orthosteric inhibitors compete with the substrate for the active site, which means their effectiveness can be reduced if substrate concentration increases.

    Allosteric

  4. Binding Site: Allosteric inhibitors bind to a site on the enzyme that is distinct and separate from the active site, known as the allosteric site.
  5. Mechanism of Action: Binding to the allosteric site induces a conformational change in the enzyme that can either reduce the affinity of the active site for the substrate or alter the enzyme's catalytic activity. This indirect interference can inhibit the enzyme's function even if the substrate is present.
  6. Non-Competitive Inhibition: Allosteric inhibitors often exhibit non-competitive inhibition, meaning their inhibitory effect is not dependent on the substrate concentration.

    Models

Many allosteric effects can be explained by the concerted MWC model put forth by Monod, Wyman, and Changeux, or by the sequential model described by Koshland, Nemethy, and Filmer. Both postulate that protein subunits exist in one of two conformations, tensed or relaxed, and that relaxed subunits bind substrate more readily than those in the tense state. The two models differ most in their assumptions about subunit interaction and the preexistence of both states. For proteins in which subunits exist in more than two conformations, the allostery landscape model described by Cuendet, Weinstein, and LeVine, can be used. Allosteric regulation may be facilitated by the evolution of large-scale, low-energy conformational changes, which enables long-range allosteric interaction between distant binding sites.

Concerted model

The concerted model of allostery, also referred to as the symmetry model or MWC model, postulates that enzyme subunits are connected in such a way that a conformational change in one subunit is necessarily conferred to all other subunits. Thus, all subunits must exist in the same conformation. The model further holds that, in the absence of any ligand, the equilibrium favors one of the conformational states, T or R. The equilibrium can be shifted to the R or T state through the binding of one ligand to a site that is different from the active site

Sequential model

The sequential model of allosteric regulation holds that subunits are not connected in such a way that a conformational change in one induces a similar change in the others. Thus, all enzyme subunits do not necessitate the same conformation. Moreover, the sequential model dictates that molecules of a substrate bind via an induced fit protocol. While such an induced fit converts a subunit from the tensed state to relaxed state, it does not propagate the conformational change to adjacent subunits. Instead, substrate-binding at one subunit only slightly alters the structure of other subunits so that their binding sites are more receptive to substrate. To summarize:
  • subunits need not exist in the same conformation
  • molecules of substrate bind via induced-fit protocol
  • conformational changes are not propagated to all subunits

    Morpheein model

The morpheein model of allosteric regulation is a dissociative concerted model.
A morpheein is a homo-oligomeric structure that can exist as an ensemble of physiologically significant and functionally different alternate quaternary assemblies. Transitions between alternate morpheein assemblies involve oligomer dissociation, conformational change in the dissociated state, and reassembly to a different oligomer. The required oligomer disassembly step differentiates the morpheein model for allosteric regulation from the classic MWC and KNF models.
Porphobilinogen synthase is the prototype morpheein.

Ensemble models

Ensemble models of allosteric regulation enumerate an allosteric system's statistical ensemble as a function of its potential energy function, and then relate specific statistical measurements of allostery to specific energy terms in the energy function. Ensemble models like the ensemble allosteric model and allosteric Ising model assume that each domain of the system can adopt two states similar to the MWC model. The allostery landscape model introduced by Cuendet, Weinstein, and LeVine allows for the domains to have any number of states and the contribution of a specific molecular interaction to a given allosteric coupling can be estimated using a rigorous set of rules. Molecular dynamics simulations can be used to estimate a system's statistical ensemble so that it can be analyzed with the allostery landscape model.

Allosteric modulation

is used to alter the activity of molecules and enzymes in biochemistry and pharmacology. For comparison, a typical drug is made to bind to the active site of an enzyme which thus prohibits binding of a substrate to that enzyme causing a decrease in enzyme activity. Allosteric modulation occurs when an effector binds to an allosteric site of an enzyme and alters the enzyme activity. Allosteric modulators are designed to fit the allosteric site to cause a conformational change of the enzyme, in particular a change in the shape of the active site, which then causes a change in its activity. In contrast to typical drugs, modulators are not competitive inhibitors. They can be positive causing an increase of the enzyme activity or negative causing a decrease of the enzyme activity. The use of allosteric modulation allows the control of the effects of specific enzyme activities; as a result, allosteric modulators are very effective in pharmacology. In a biological system, allosteric modulation can be difficult to distinguish from modulation by substrate presentation.

Energy sensing model

An example of this model is seen with the Mycobacterium tuberculosis, a bacterium that is perfectly suited to adapt to living in the macrophages of humans. The enzyme's sites serve as a communication between different substrates. Specifically between AMP and G6P. Sites like these also serve as a sensing mechanism for the enzyme's performance.

Positive modulation

Positive allosteric modulation occurs when the binding of one ligand enhances the attraction between substrate molecules and other binding sites. An example is the binding of oxygen molecules to hemoglobin, where oxygen is effectively both the substrate and the effector. The allosteric, or "other", site is the active site of an adjoining protein subunit. The binding of oxygen to one subunit induces a conformational change in that subunit that interacts with the remaining active sites to enhance their oxygen affinity.
Another example of allosteric activation is seen in cytosolic IMP-GMP specific 5'-nucleotidase II, where the affinity for substrate GMP increases upon GTP binding at the dimer interface.

Negative modulation

Negative allosteric modulation occurs when the binding of one ligand decreases the affinity for substrate at other active sites. For example, when 2,3-BPG binds to an allosteric site on hemoglobin, the affinity for oxygen of all subunits decreases. This is when a regulator is absent from the binding site.
Direct thrombin inhibitors provides an excellent example of negative allosteric modulation. Allosteric inhibitors of thrombin have been discovered that could potentially be used as anticoagulants.
Another example is strychnine, a convulsant poison, which acts as an allosteric inhibitor of the glycine receptor. Glycine is a major post-synaptic inhibitory neurotransmitter in mammalian spinal cord and brain stem. Strychnine acts at a separate binding site on the glycine receptor in an allosteric manner; i.e., its binding lowers the affinity of the glycine receptor for glycine. Thus, strychnine inhibits the action of an inhibitory transmitter, leading to convulsions.
Another instance in which negative allosteric modulation can be seen is between ATP and the enzyme phosphofructokinase within the negative feedback loop that regulates glycolysis. Phosphofructokinase is an enzyme that catalyses the third step of glycolysis: the phosphorylation of fructose-6-phosphate into fructose 1,6-bisphosphate. PFK can be allosterically inhibited by high levels of ATP within the cell. When ATP levels are high, ATP will bind to an allosteric site on phosphofructokinase, causing a change in the enzyme's three-dimensional shape. This change causes its affinity for substrate at the active site to decrease, and the enzyme is deemed inactive. This causes glycolysis to cease when ATP levels are high, thus conserving the body's glucose and maintaining balanced levels of cellular ATP. In this way, ATP serves as a negative allosteric modulator for PFK, despite the fact that it is also a substrate of the enzyme.