Figure 15–8 The regulation of a monomeric GTPase. GTPase-activating proteins (GAPs) inactivate the protein by stimulating it to hydrolyze its bound GTP to GDP, which remains tightly bound to the inactivated GTPase. Guanine nucleotide exchange factors (GEFs) activate the inactive protein by stimulating it to release its GDP; because the concentration of GTP in the cytosol is 10 times greater than the concentration of GDP, the protein rapidly binds GTP and is thereby activated.
Figure 15–9 A sequence of two inhibitory signals produces a positive signal.
In this simple signaling system, a transcription regulator is kept in an inactive state by a bound inhibitor protein. In response to some upstream signal, a protein kinase is activated and phosphorylates the inhibitor, causing its dissociation from the transcription regulator and thereby activating gene expression.
This signaling pathway can be diagrammed as a sequence of four steps, including two sequential inhibitory steps that are equivalent to a single activating step.
Cells in a population often exhibit random variation in the concentration or activity of their intracellular signaling molecules. Similarly, individual molecules in a large population of molecules vary in their activity or interactions with other molecules. This signal variability introduces another form of noise that can interfere with the precision and efficiency of signaling. Most signaling systems, however, are built to generate remarkably robust and precise responses even when upstream signals are variable or even when some components of the system are disabled. In many cases, this robustness depends on the presence of backup mechanisms: for example, a signal might employ two parallel pathways to activate a single common downstream target protein, allowing the response to occur even if one pathway is crippled.
One simple and effective strategy for enhancing the specificity of interactions between signaling molecules is to localize them in the same part of the cell or even within large protein complexes, thereby ensuring that they interact only with each other and not with inappropriate partners. Such mechanisms often involve scaffold proteins, which bring together groups of interacting signaling proteins into signaling complexes, often before a signal has been received (Figure 15–10A). Because the scaffold holds the proteins in close proximity, they can interact at high local concentrations and be sequentially activated rapidly, efficiently, and selectively in response to an appropriate extracellular signal, avoiding unwanted cross-talk with other signaling pathways.
In other cases, such signaling complexes form only transiently in response to an extracellular signal and rapidly disassemble when the signal is gone. They often assemble around a receptor after an extracellular signal molecule has activated it. In many of these cases, the cytoplasmic tail of the activated receptor is phosphorylated during the activation process, and the phosphorylated amino acids then serve as docking sites for the assembly of other signaling proteins (Figure 15–10B). In yet other cases, receptor activation leads to the production of modified phospholipid molecules (called phosphoinositides) in the adjacent plasma membrane, which then recruit specific intracellular signaling proteins to this region of membrane, where they are activated (Figure 15–10C).
Simply bringing intracellular signaling proteins together into close proximity is sometimes sufficient to activate them. Thus, induced proximity, where a signal triggers assembly of a signaling complex, is commonly used to relay signals from protein to protein along a signaling pathway. The assembly of such signaling complexes depends on various highly conserved, small interaction domains, which are found in many intracellular signaling proteins. Each of these compact protein modules binds to a particular structural motif in another protein or lipid. The recognized motif in the interacting protein can be a short peptide sequence, a covalent modification (such as a phosphorylated amino acid), or another protein domain. The use of modular interaction domains presumably facilitated the evolution of new signaling pathways; because it can be inserted at many locations in a protein without disturbing the protein’s folding or function, a new interaction domain added to an existing signaling protein could connect the protein to additional signaling pathways.