In biology, scaffold proteins are crucial regulators of many key signaling pathways. Although scaffolds are not strictly defined in function, they are known to interact and/or bind with multiple members of a signaling pathway, tethering them into complexes. In such pathways, they regulate signal transduction and help localize pathway components (organized in complexes) to specific areas of the cell such as the plasma membrane, the cytoplasm

Cytoplasm

The cytoplasm is a small gel-like substance residing between the cell membrane holding all the cell's internal sub-structures , except for the nucleus. All the contents of the cells of prokaryote organisms are contained within the cytoplasm...

, the nucleus

Cell nucleus

In cell biology, the nucleus is a membrane-enclosed organelle found in eukaryotic cells. It contains most of the cell's genetic material, organized as multiple long linear DNA molecules in complex with a large variety of proteins, such as histones, to form chromosomes. The genes within these...

, the Golgi

Golgi

Golgi may refer to:*Camillo Golgi , Italian physician and scientist after which the following terms are named:**Golgi apparatus , an organelle in the eukaryotic cell...

, endosomes, and the mitochondria.

History

The first examples of signaling scaffold proteins were receptor tyrosine kinase

Receptor tyrosine kinase

Receptor tyrosine kinases s are the high-affinity cell surface receptors for many polypeptide growth factors, cytokines, and hormones. Of the 90 unique tyrosine kinase genes identified in the human genome, 58 encode receptor tyrosine kinase proteins....

s like epidermal growth factor receptor

Epidermal growth factor receptor

The epidermal growth factor receptor is the cell-surface receptor for members of the epidermal growth factor family of extracellular protein ligands...

s and platelet-derived growth factor receptor

Platelet-derived growth factor receptor

Platelet-derived growth factor receptors are cell surface tyrosine kinase receptors for members of the platelet-derived growth factor family. PDGF subunits -A and -B are important factors regulating cell proliferation, cellular differentiation, cell growth, development and many diseases including...

. Upon ligand

Ligand

In coordination chemistry, a ligand is an ion or molecule that binds to a central metal atom to form a coordination complex. The bonding between metal and ligand generally involves formal donation of one or more of the ligand's electron pairs. The nature of metal-ligand bonding can range from...

 binding to such receptors, tyrosine autophosphorylation occurs in the receptor’s cytoplasmic domain specifically at sites where SRC homology 2 (SH2)-domain-containing proteins can bind. In this case, the receptor’s cytoplasmic domain acts as a scaffold, recruiting signaling proteins and initially localizing the signaling response to the plasma membrane. The subsequent endocytosis

Endocytosis

Endocytosis is a process by which cells absorb molecules by engulfing them. It is used by all cells of the body because most substances important to them are large polar molecules that cannot pass through the hydrophobic plasma or cell membrane...

 of the activated receptor and its intracellular trafficking further localizes the signal to other specific areas of the cell.

Function

Scaffold proteins act in at least four ways: tethering signaling components, localizing these components to specific areas of the cell, regulating signal transduction by coordinating positive

Positive feedback

Positive feedback is a process in which the effects of a small disturbance on a system include an increase in the magnitude of the perturbation. That is, A produces more of B which in turn produces more of A. In contrast, a system that responds to a perturbation in a way that reduces its effect is...

 and negative feedback

Negative feedback

Negative feedback occurs when the output of a system acts to oppose changes to the input of the system, with the result that the changes are attenuated. If the overall feedback of the system is negative, then the system will tend to be stable.- Overview :...

 signals, and insulating correct signaling proteins from competing proteins..

Tethering signaling components

This particular function is considered a scaffold’s most basic function. Scaffolds assemble signaling components of a cascade

Biochemical cascade

A biochemical cascade is a series of chemical reactions in which the products of one reaction are consumed in the next reaction. There are several important biochemical cascade reactions in biochemistry, including the enzymatic cascades, such as the coagulation cascade and the complement system,...

 into complexes. This assembly may be able to enhance signaling specificity by preventing unnecessary interactions between signaling proteins, and enhance signaling efficiency by increasing the proximity and effective concentration of components in the scaffold complex. A common example of how scaffolds enhance specificity is a scaffold that binds a protein kinase and its substrate, thereby ensuring specific kinase phosphorylation. Additionally, some signaling proteins require multiple interactions for activation and scaffold tethering may be able to convert these interactions into one interaction that results in multiple modifications. Scaffolds may also be catalytic as interaction with signaling proteins may result in allosteric changes of these signaling components. Such changes may be able to enhance or inhibit the activation of these signaling proteins. An example is the Ste5 scaffold in the mitogen-activated protein kinase (MAPK

Mitogen-activated protein kinase

Mitogen-activated protein kinases are serine/threonine-specific protein kinases that respond to extracellular stimuli and regulate various cellular activities, such as gene expression, mitosis, differentiation, proliferation, and cell survival/apoptosis.-Activation:MAP kinases are activated...

) pathway. Ste5 has been proposed to direct mating signaling through the Fus3 MAPK by catalytically unlocking this particular kinase for activation by its MAPKK Ste7.

Localization of signaling components in the cell

Scaffolds localize the signaling reaction to a specific area in the cell, a process that could be important for the local production of signaling intermediates. A particular example of this process is the scaffold, A-kinase anchor proteins (AKAPs), which target cyclic AMP-dependent protein kinase (PKA) to various sites in the cell. This localization is able to locally regulate PKA and results in the local phosphorylation by PKA of its substrates.

Coordinating positive and negative feedback

Many hypotheses about how scaffolds coordinate positive and negative feedback come from engineered scaffolds and mathematical modeling. In three-kinase signaling cascades, scaffolds bind all three kinases, enhancing kinase specificity and restricting signal amplification by limiting kinase phosphorylation to only one downstream target. These abilities may be related to stability of the interaction between the scaffold and the kinases, the basal phosphatase

Phosphatase

A phosphatase is an enzyme that removes a phosphate group from its substrate by hydrolysing phosphoric acid monoesters into a phosphate ion and a molecule with a free hydroxyl group . This action is directly opposite to that of phosphorylases and kinases, which attach phosphate groups to their...

 activity in the cell, scaffold location, and expression levels of the signaling components.

Insulating correct signaling proteins from inactivation

Signaling pathways are often inactivated by enzymes that reverse the activation state and/or induce the degradation of signaling components. Scaffolds have been proposed to protect activated signaling molecules from inactivation and/or degradation. Mathematical modeling has shown that kinases in a cascade without scaffolds have a higher probability of being dephosphorylated by phosphatases before they are even able to phosphorylate downstream targets.

Scaffold protein summary

Scaffold Proteins	Pathway	Potential Functions	Description
KSR KSR KSR is an initialism that may mean:* Kendall Square Research, a supercomputer company headquartered originally in Kendall Square in Cambridge, Massachusetts* Keyboard Send Receive, a type of teleprinter that contains a keyboard but no punched tape equipment...	MAPK	Assembly and localization of the RAS-ERK pathway	One of the best studied signaling pathways in biology is the RAS-ERK MAPK/ERK pathway The MAPK/ERK pathway is a chain of proteins in the cell that communicates a signal from a receptor on the surface of the cell to the DNA in the nucleus of the cell. The signal starts when a growth factor binds to the receptor on the cell surface and ends when the DNA in the nucleus expresses a...  pathway in which the RAS G-protein activates the MAPKKK RAF C-Raf RAF proto-oncogene serine/threonine-protein kinase also known as proto-oncogene c-RAF or simply c-Raf is an enzyme that in humans is encoded by the RAF1 gene. The c-Raf protein functions in the MAPK/ERK signal transduction pathway as part of a protein kinase cascade... , which activates the MAPKK MAPK/ERK kinase 1 (MEK1), which then activates the MAPK ERK Extracellular signal-regulated kinases In molecular biology, extracellular-signal-regulated kinases or classical MAP kinases are widely expressed protein kinase intracellular signalling molecules that are involved in functions including the regulation of meiosis, mitosis, and postmitotic functions in differentiated cells... . Several scaffold proteins have been identified to be involved in this pathway and other similar MAPK pathways. One such scaffold protein is KSR, which is the most probable equivalent of the well-studied yeast MAPK scaffold protein Ste5. It is a positive regulator of the pathway and binds many proteins in the pathway, including all three kinases in the cascade. KSR has been shown to be localized to the plasma membrane during cell activation, thereby playing a role in assembling the components of the ERK pathway and in localizing activated ERK to the plasma membrane.
MEKK1	MAPK	Assembly and localization of the death receptor signalosome	Other scaffold proteins include B-cell lymphoma 10 (BCL-10 BCL10 B-cell lymphoma/leukemia 10 is a protein that in humans is encoded by the BCL10 gene.-Interactions:BCL10 has been shown to interact with CARD10, CARD11, MALT1, TRAF2, IKBKG and CARD9.-Further reading:... ) and MEK kinase 1 (MEKK1), which have roles in the JUN N-terminal kinase (JNK) pathway.
BCL-10	MAPK	Assembly and specificity of JNK
AHNAK-1	Calcium signaling Calcium signaling Calcium is a common signaling mechanism, as once it enters the cytoplasm it exerts allosteric regulatory effects on many enzymes and proteins...	Assembly and localization of calcium channels	Calcium signaling is essential for the proper function of immune cells. Recent studies have shown that the scaffold protein, AHNAK1, is important for efficient calcium signaling and NFAT NFAT Nuclear factor of activated T-cells is a general name applied to a family of transcription factors shown to be important in immune response. One or more members of the NFAT family is expressed in most cells of the immune system...  activation in T cells through its ability to properly localize calcium channels at the plasma membrane [14]. In non-immune cells, AHNAK1 has also been shown to bind calcium channels with phospholipase Cγ (PLC-γ Phospholipase C Phosphoinositide phospholipase C is a family of eukaryotic intracellular enzymes that play an important role in signal transduction processes. In general, this enzyme is denoted as Phospholipase C, although three other families of phospholipase C enzymes have been identified in bacteria and in... ) and PKC Protein kinase C Protein kinase C also known as PKC is a family of enzymes that are involved in controlling the function of other proteins through the phosphorylation of hydroxyl groups of serine and threonine amino acid residues on these proteins. PKC enzymes in turn are activated by signals such as increases in... . Calcium binding proteins often quench much of the entering calcium, so linking these calcium effectors may be especially important when signals are induced by a weak calcium influx.
HOMER Homer In the Western classical tradition Homer , is the author of the Iliad and the Odyssey, and is revered as the greatest ancient Greek epic poet. These epics lie at the beginning of the Western canon of literature, and have had an enormous influence on the history of literature.When he lived is...	Calcium signaling	Inhibition of NFAT activation	Another example of a scaffold protein that modulates calcium signaling is proteins of the HOMER family. The HOMER proteins have been shown to compete with calcineurin Calcineurin Calcineurin is a protein phosphatase also known as protein phosphatase 3, PPP3CA, and calcium-dependent serine-threonine phosphatase, and formerly known as protein phosphatase 2B . It activates the T cells of the immune system and can be blocked by drugs...  to bind to the N terminus of NFAT in activated T cells. Through this competition, the HOMER proteins are able to reduce NFAT activation, which also reduces the production of the IL-2 Interleukin 2 Interleukin-2 is an interleukin, a type of cytokine immune system signaling molecule, which is a leukocytotrophic hormone that is instrumental in the body's natural response to microbial infection and in discriminating between foreign and self...  cytokine. In contrast, HOMER proteins have also been shown to positively regulate calcium signaling in neurons by linking the glutamate receptor Glutamate receptor Glutamate receptors are synaptic receptors located primarily on the membranes of neuronal cells. Glutamate is one of the 20 amino acids used to assemble proteins and as a result is abundant in many areas of the body, but it also functions as a neurotransmitter and is particularly abundant in the...  with triphosphate receptors in the endoplasmic reticulum.
Pellino	Innate Immune Signaling	Assembly of the TLR signalosome	Evidence exists that Pellino proteins function as scaffold proteins in the important innate immune signaling pathway, the Toll-like receptor (TLR Toll-like receptor Toll-like receptors are a class of proteins that play a key role in the innate immune system. They are single, membrane-spanning, non-catalytic receptors that recognize structurally conserved molecules derived from microbes... ) pathway. Much Pellino function is speculation; however, Pellino proteins can associate with IRAK1, TRAF6, and TAK1 following IL-1R activation, indicating that they may assemble and localize components of the TLR pathway near its receptor.
NLRP NLRP NLRP can refer to:* NLRP1, a human gene that encodes the NACHT, LRR and PYD domains-containing protein 1* NLRP2, a human gene that encodes the NACHT, LRR and PYD domains-containing protein 2...	Innate Immune Signaling	Assembly of the inflammasome	The NLR family is a highly conserved and large family of receptors involved in innate immunity. The NLRP (NLR family, pyrine domain-containing) family of receptors function as scaffolds by assembling the inflammasome, a complex that leads to the secretion of pro-inflammatory cytokines such as IL-18 and IL-1β.
DLG1 DLG1 Disks large homolog 1 , also known as synapse-associated protein 97 or SAP97, is a protein that in humans is encoded by the SAP97 gene....	T-cell receptor signaling	Assembly and localization of TCR signaling molecules, activation of p38	DLG1 is highly conserved in immune cells and is important for T-cell activation in the periphery. It is recruited to the immunological synapse and links the ζ-chain of the T-cell receptor (TCR T cell receptor The T cell receptor or TCR is a molecule found on the surface of T lymphocytes that is responsible for recognizing antigens bound to major histocompatibility complex molecules... ) to CBL, WASP, p38, LCK, VAV1, and ZAP70. This data suggests that DLG1 plays a role in linking TCR signaling machinery with cytoskeleton regulators and also suggests a role in alternatively activating the p38 pathway. However, it is unclear to whether DLG1 positively or negatively regulates T-cell activation.
Spinophilin	Dendritic cell Dendritic cell Dendritic cells are immune cells forming part of the mammalian immune system. Their main function is to process antigen material and present it on the surface to other cells of the immune system. That is, dendritic cells function as antigen-presenting cells...  signaling	Assembly of DC immunological-synapse proteins	Spinophilin is involved in dendritic cell function specifically in the formation of immunological synapses. Spinophilin is recruited to the synapse following dendritic cell contact with a T cell. This recruitment seems to be important because without spinophilin, dendritic cells cannot activate T cells in vitro or in vivo. How spinophilin facilitates antigen presentation in this case is still unknown though it is possible that spinophilin regulates the duration of cell contact in the synapse or regulates the recycling of co-stimulatory molecules in the cell like MHC molecules.
Plant FLU regulatory protein	Coordination of negative feedback during protochlorophyllide Protochlorophyllide Protochlorophyllide, or monovinyl protochlorophyllide, is an immediate precursor of chlorophyll a that lacks the phytol side-chain of chlorophyll. Unlike chlorophyll, protochlorophyllide is highly fluorescent; mutants that accumulate it glow red if irradiated with blue light...   biosynthesis.	Assembly and localization of the pathway that turns of synthesis of highly toxic protochlorophyllide Protochlorophyllide Protochlorophyllide, or monovinyl protochlorophyllide, is an immediate precursor of chlorophyll a that lacks the phytol side-chain of chlorophyll. Unlike chlorophyll, protochlorophyllide is highly fluorescent; mutants that accumulate it glow red if irradiated with blue light... , a precursor of chlorophyll Chlorophyll Chlorophyll is a green pigment found in almost all plants, algae, and cyanobacteria. Its name is derived from the Greek words χλωρος, chloros and φύλλον, phyllon . Chlorophyll is an extremely important biomolecule, critical in photosynthesis, which allows plants to obtain energy from light... .	Synthesis of protochlorophyllide must be strictly regulated as its conversion into chlorophyll requires light. FLU regulatory protein is located in thylakoid Thylakoid A thylakoid is a membrane-bound compartment inside chloroplasts and cyanobacteria. They are the site of the light-dependent reactions of photosynthesis. Thylakoids consist of a thylakoid membrane surrounding a thylakoid lumen. Chloroplast thylakoids frequently form stacks of disks referred to as... membrane and only contains several protein-protein interaction sites without catalytic activity. Mutants lacking this protein overaccumulate protochlorophyllide in the darkness. The interaction partners are unknown. The protein underwent simplification during evolution.