Báo cáo khoa học: Functional classification of scaffold proteins and related molecules pptx

MINIREVIEW
Functional classification of scaffold proteins and related
molecules
La
´
szlo
´
Buday
1,2
and Pe
´
ter Tompa
1
1 Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary
2 Department of Medical Chemistry, Semmelweis University Medical School, Budapest, Hungary
Introduction
Cells use a multitude of signaling proteins to alter cel-
lular behavior in response to changes in their external
and internal environment. Because of the multiplicity
and broad substrate specificity of signaling enzymes, it
is of immense importance to understand how the cell
achieves efficiency and accuracy in signaling. It is
generally accepted that the primary mechanism is to
promote the proximity of signaling enzymes by specific
binding to a special class of regulatory proteins [1–4].
These proteins come under a variety of names, such as
scaffold, adaptor, anchor and docking, but invariably
function by ‘enforced proximity’, i.e. by binding at
least two signaling enzymes together and directing,
coordinating and regulating their action (Fig. 1). In
Keywords

adaptor; anchor; docking protein; kinase;
multidomain protein; phosphatase; protein
interaction; scaffold; signaling; structural
disorder
Correspondence
L. Buday and P. Tompa, Institute of
Enzymology, Hungarian Academy of
Sciences, 1518 Budapest, P.O. Box 7,
Hungary
Fax: +361 466 5465
Tel: +361 279 3115; +361 279 3143
E-mail: ;
(Received 14 May 2010, revised 3 August
2010, accepted 18 August 2010)
doi:10.1111/j.1742-4658.2010.07864.x
In this series of four minireviews the field of scaffold proteins and proteins
of similar molecular ⁄ cellular functions is overviewed. By binding and bring-
ing into proximity two or more signaling proteins, these proteins direct the
flow of information in the cell by activating, coordinating and regulating
signaling events in regulatory networks. Here we discuss the categories of
scaffolds, anchors, docking proteins and adaptors in some detail, and using
many examples we demonstrate that they cover a wide range of functional
modes that appear to segregate into three practical categories, simple pro-
teins binding two partners together (adaptors), larger multidomain proteins
targeting and regulating more proteins in complex ways (scaffold ⁄ anchor-
ing proteins) and proteins specialized to initiate signaling cascades by local-
izing partners at the cell membrane (docking proteins). It will also be
shown, however, that the categories partially overlap and often their names
are used interchangeably in the literature. In addition, although not usually
considered as scaffolds, several other proteins, such as regulatory proteins

with catalytic activity, phosphatase targeting subunits, E3 ubiquitin ligases,
ESCRT proteins in endosomal sorting and DNA damage sensors also func-
tion by bona fide scaffolding mechanisms. Thus, the field is in a state of
continuous advance and expansion, which demands that the classification
scheme be regularly updated and, if needed, revised.
Abbreviations
AKAP, A-kinase anchoring protein; DAPP, dual-adapter for phosphotyrosine and 3-phosphoinositides; DD, death domain; FADD,
Fas-associated protein with death domain; MAGUK, membrane-associated guanylate kinase; MYPT1, myosin phosphatase targeting subunit
1; Nck, non-catalytic region of tyrosine kinase adaptor protein; PDZ, post-synaptic density, disc large, zo-1 protein; PH, pleckstrin homology;
PSD, post-synaptic density; RTK, receptor tyrosine kinase; SH2, Src homology 2; SH3, Src homology 3; SKAP, Src kinase-associated
phosphoprotein.
4348 FEBS Journal 277 (2010) 4348–4355 ª 2010 The Authors Journal compilation ª 2010 FEBS
the literature, the names are often used interchange-
ably, which indicates that the functions of the proteins
in the four categories overlap significantly and they are
often difficult to distinguished. This article, and the
following three in this minireview series provide a con-
cise functional description of scaffold proteins and
their kin, in general, and their distinct classes, in par-
ticular, encompassing scaffolds [5], docking proteins
[6], anchors [7] and adaptors (this article).
We also point out overlaps and inconsistencies in
terminology, to show that members of this entire
functional class occupy positions along a rather contin-
uous functional spectrum. We also describe targeting
subunits of phosphatases, which have a function in
close analogy with that of anchors. In addition, we
also show that there are many other proteins that
function using scaffolding mechanisms, and ought to
be considered in extending the classification scheme of

these regulatory proteins. It will be addressed that
scaffold proteins and their kin not only bring signaling
proteins together, but also regulate the flow of signal-
ing information using a variety of mechanisms, owing
to which proteins in this broad functional class no
longer emerge as passive connectors, but active regula-
tory elements shaping the response put out by signal-
ing networks. We suggest that this active role may also
be linked with extended structural disorder of the
proteins [8–10], which enables dynamic communication
between their distinct binding and functional elements
(Fig. 1 and Table 1).
It should also be made clear that because of space
limitations this minireview is not comprehensive, and
the reader is directed to many excellent recent reviews
[1–4,11], and the other minireviews in this series [5–7]
for further details and insight into this field of continu-
ous advance.
Scaffold/anchoring proteins
Scaffold and anchoring proteins are reviewed in two of
the other minireviews in this series [5,7]. Here we pro-
vide a short overview of their most notable examples,
to demonstrate that the distinction between these two
categories is historical, rather than structural or
functional.
Scaffold proteins may be considered as the founders
of this functional class, epitomizing the very essence of
the action of signaling regulatory proteins [5]. They
are defined as proteins organizing signaling complexes
by binding at least two signaling enzymes together and

promoting their communication by proximity. Classi-
cally, they have been regarded as passive platforms for
the assembly of signalosomes, but more recently it has
become clear that they play rather active regulatory
roles (Fig. 1 and Table 1). They may operate by four
basic mechanisms, such as enforced proximity, combi-
natorial use of elements, dynamic regulation and con-
formational fine-tuning [4,5]. As demonstrated by one
of the best characterized scaffolds, Ste5, which regu-
lates the extracellular signal-regulated kinase ⁄ mitogen-
activated protein kinase pathway in yeast, their func-
tion may be to assemble complexes, enforce restricted
intracellular localization, provide allosteric feedback
and feed-forward regulation, and offer protection
against degradation [3]. They may enable context-
dependent fine-tuning of pre-existing signaling
A
B
Adaptor
A
Docking
P
P
P
P
C
A
B
C
Scaffold/anchor

B
Fig. 1. Mechanisms of scaffold proteins and their kin. This scheme
outlines the most important aspects of the function of modular regu-
latory proteins in the four (three) closely related categories. In all cat-
egories, the proteins regulate signaling pathways by binding several
of the components and targeting ⁄ regulating their action in complex
ways (regulatory interactions ⁄ modifications marked by arrows).
Within this generalized scheme, there are three distinct types of
behavior. (A) Adaptors are usually small, and have two binding
regions to target the action of two bound enzymes. (B) Scaf-
folds ⁄ anchors are large multidomain proteins with a lot of structural
disorder, able to bind and regulate several members of a signaling
pathway. (C) Docking proteins have a similar structural and functional
outline, their distinguishing feature being their ability to localize at
the membrane next to an activating receptor, to which they bind in a
phosphorylation-dependent manner. In the entire class of proteins, a
high level of structural disorder (43.3% on average; Table 1) enables
key functional attributes, such as binding of several partners, to be
combined. A, B and C marks general proteins. P, phosphate.
L. Buday and P. Tompa Functional classification of scaffold proteins
FEBS Journal 277 (2010) 4348–4355 ª 2010 The Authors Journal compilation ª 2010 FEBS 4349
pathways or create new pathways using novel combi-
nations of signaling elements. Scaffolds are extremely
heterogeneous in structure and function, which may
significantly overlap with those of other classes. A few
selected examples (Table 1; cf. [5]) show that they
often have separated binding domains for protein–pro-
tein interactions, and also have a high level of struc-
tural disorder, which may provide both short binding
regions and flexibility for dynamic regulatory rear-

rangements.
These principles are also apparent in scaffolds that
operate in neuronal and immune cells, which are
highly polarized and form complex structures termed
synapses. Synapses contain a plethora of receptors, ion
channels and signaling proteins for sensing and pro-
cessing extracellular signals, organized and connected
to the cytoskeleton to form large complexes, such as
the post-synaptic density (PSD) complex. The best
known of the scaffolds are the membrane-associated
guanylate kinase (MAGUK) proteins, which have vari-
ous numbers of post-synaptic density, disc large, zo-1
protein (PDZ) domains, an Src homology (SH)3
domain and a C-terminal guanylate kinase domain [1].
The best studied MAGUK in T cells is DLG1,
whereas in neurons it is PSD95, with notable similari-
ties in function. PSD95 is the most abundant scaffold
in the PSD, it has three PDZ domains, and binds
a variety of receptors ⁄ channels, cytoskeletal and
Table 1. Scaffold proteins and their kin. Representatives of the four categories of scaffold proteins and their relatives are presented. The
length of the human (unless indicated otherwise) isoform is given, along with its typical domains, binding partners and percent structural
disorder, as predicted by the IUPred algorithm [42]. Protein–protein interaction domains and interaction partners have been taken from the
literature [1–7,22] and the list is not intended to be exhaustive. AKAP, A-kinase anchoring protein; Caskin 1, CASK-interacting protein 1;
DED, death effector domain; DLG(1), discs, large homolog (1); Dok1, docking protein 1; ERK, extracellular signal-regulated kinase; FADD,
Fas-associated protein with death domain; FRS, FGF receptor substrate; Gab,Grb2-associated binder; Grb2, growth factor receptor-bound
protein 2; IRS, insulin receptor substrate; KSR, kinase suppressor of Ras; MYPT1, myosin phosphatase targeting subunit 1; Nck1, non-cata-
lytic region of tyrosine kinase adaptor protein 1; PDZ, post-synaptic density, disc large, zo-1 protein (domain); PH, pleckstrin homology
domain; PI3-kinase, phosphoinositide-3-kinase; PKA, protein kinase A; PKC, protein kinase C; PP1, protein phosphatase 1; PSD, post-synaptic
density; PTB, phosphotyrosine binding domain; RACK, receptor for activated C kinase; SARA, SMAD-anchor for receptor activation; SH2, Src
homology 2 domain; SH3, Src homology 3 domain; Ste5, sterile 5; TGFb, transforming growth factor beta.

Protein
Length
(number of
amino acids) Domain(s) Protein partners Disorder (%)
Scaffold
ste5 (yeast) 917 PHD, PH Ste4, Ste7, Ste20, Ste11, FUS3 275 (30.0)
KSR 921 Protein kinase, zinc finger,
Serpin
Raf, MEK1, ERK, 14-3-3, PP2A 321 (34.9)
PSD95 724 PDZ, SH3, GK glutamate (NMDA) receptor,
K+ channels, nNOS, NGL-2, SALM2,
ADAM22, SYNGAP
95 (13.1)
DLG1 904 PDZ, SH3, GK, L27 Ezrin, CASK, PTEN 267 (29.5)
Shank1 2161 ANK repeats, PDZ, SAM, SH3 IRSp53, Sharpin, Abp1, Homer 1515 (70.1)
Caskin1 1431 ANK repeats, SAM, SH3 CASK, Nck, Abi2 996 (69.6)
SARA 1425 FYVE-type zinc finger SMAD2, SMAD3, TGF-beta receptor 441 (30.9)
Anchoring
AKAP150, rat 714 – PKA, PKC, SAP97, glutamate (AMPA) receptor 611 (85.6)
mAKAP 2319 Spectrin repeats PKA, Epac1, Rac1, ERK5 1091 (47.0)
RACK1 317 WD repeats PKC, Src, integrin, dynamin1 2 (0.0)
MYPT1 1030 Ankirin repeats PP1CA, ROCK1, Ezrin, Merlin, Synaptophysin 722 (70.1)
Docking
IRS1 1242 PH, PTB PI-P
3
, Grb2, Nck, PI 3-kinase, SHP2 971 (78.2)
FRS2 508 PTB FGFR, NGFR, Shc1, Grb2, PTPN11 372 (73.2)
Gab1 694 PH, MBD Grb2, c-Met, SHP2, PI 3-kinase, PLCc 544 (78.4)
Dok1 481 PH, PTB Abl, Bcr-Abl, p120Ras-GAP 207 (43.0)
Adaptor

Grb2 217 SH2, SH3 EGFR, LAT, c-Met, Cbl, Dynamin, N-WASP,
SAM68, SLP-76, Sos, Synapsin, Vav
0 (0)
Nck1 377 SH2, SH3 Abl, Cbl, Dynamin, FAK, NAK, NAP1, N-WASP,
PAK, PRK2, Sos
48 (12.7)
FADD 208 DD, DED Fas receptor, TNFR-1, procaspase-8, procaspase-10 28 (13.5)
Functional classification of scaffold proteins L. Buday and P. Tompa
4350 FEBS Journal 277 (2010) 4348–4355 ª 2010 The Authors Journal compilation ª 2010 FEBS
signaling proteins (Table 1). Because of its multiplicity
of binding partners, PSD95 functions in receptor
clustering, targeting receptor action on Ras and Rho
signaling, and regulating receptor modification under-
scoring dynamics of synaptic function. A similar logic
applies to DLG1 (synapse-associated protein-97),
which regulates immunological synapses by physically
linking T-cell receptor signaling to cytoskeletal rear-
rangements. Table 1 lists a few further scaffolds, all of
which are modular with several protein–protein
interaction domains and motifs embedded in and ⁄ or
connected by long disordered regions, such as Shank1
and Caskin1 in neuronal PSD or SARA in transform-
ing growth factor beta signaling.
Scaffolds epitomize the very essence of the entire
family of signaling proteins, first appreciated in tyro-
sine kinase signaling where adaptors, scaffolds or
enzymes are recruited to the autophosphorylated
receptor tyrosine kinases (RTKs). Cytosolic kinases
and phosphatases, however, also require strict control
of their activity and subcellular localization, which is

achieved through anchoring proteins, originally defined
as proteins targeting the action of protein kinase A
(A-kinase anchoring proteins; AKAPs), on specific
substrates [7]. They are usually long proteins with a lot
of structural disorder (Fig. 1 and Table 1), with func-
tional attributes difficult to clearly distinguish from
that of scaffolds (described in detail in ref. [7]). In
addition to AKAPs, protein kinase C also interacts
with a family of anchor proteins called receptors for
activated C kinase.
Cytosolic Ser ⁄ Thr phosphatases are also directed
into signaling networks by mechanisms similar to that
of protein kinase A and protein kinase C. For exam-
ple, functional protein phosphatase 1 consists of a cat-
alytic subunit and a regulatory subunit. The regulatory
subunits target the catalytic subunit to specific cellular
compartments and modulate substrate specificity [12].
One of the best characterized regulatory subunits is the
myosin phosphatase target subunit (MYPT1). A num-
ber of regulatory proteins, as well as Ser ⁄ Thr kinases,
can associate with MYPT1, suggesting that similarly
to AKAPs and receptors for activated C kinase, the
function of MYPT1 is much broader than simply tar-
geting protein phosphatase 1 to myosin II [13].
Docking proteins
As outlined in the accompanying minireview by Brum-
mer et al. [6], docking proteins were originally defined
as accessory proteins in RTK signaling with a mem-
brane-targeting region, a protein–protein interaction
site for receptor binding and an extended region with

several Tyr residues for receptor-dependent phosphory-
lation (Fig. 1 and Table 1). This outline applies to all
four major families of classical docking protein, such
as the Grb2-associated binder ⁄ daughter of sevenless
(Gab ⁄ DOS), insulin receptor substrate, FGF receptor
substrate and docking protein families [6]. Docking
proteins are recruited to the site of RTK activation at
the plasma membrane, they reinforce binding by virtue
of a receptor-binding domain (often a phosphotyro-
sine-binding domain) and undergo multiple Tyr-phos-
phorylation (there are more than five Tyr
phosphorylation sites in at least one of the family
members). Phosphorylation of Tyr residues is rather
specific to certain RTKs, but may also proceed by
cytoplasmic tyrosine kinases. Tyr-phosphorylated
docking proteins recruit SH2-domain-containing sig-
naling components to initiate specific signal cascades,
and they coordinate and regulate Tyr kinase signaling
events, and also display dynamic regulatory phenom-
ena described in more detail for scaffold proteins (for
details see ref. [6]).
There are also other, atypical docking proteins [6],
which lack the lipid-binding domain but have N-termi-
nal domains ⁄ regions that help them localize at the
plasma membrane next to activating receptors, and
also contain several Tyr residues that undergo phos-
phorylation and recruitment of signaling proteins.
Although the function of these proteins (linker for
activated T cells, Crk-associated substrate, SLP65) is
closely related to other docking proteins, they appear

to be better classified as scaffolds.
Adaptor proteins
The term adaptor protein is generally used for low
molecular mass molecules that serve to link two func-
tional members of a catalytic pathway (Fig. 1 and
Table 1). Adaptors either possess two domains involved
in protein–protein interactions or use two regions com-
posed of two to three domains. The first group of adap-
tor proteins identified was the family of SH2 ⁄ SH3
domain-containing proteins, including growth factor
receptor-bound protein 2, Crk, CrkL and non-catalytic
region of tyrosine kinase adaptor protein 1 (Nck) [14].
Their SH2 domain binds specific phosphotyrosine resi-
dues on activated receptors or their substrates, whereas
their SH3 domains bind proline-rich motifs on down-
stream target proteins. Interestingly, this family of
adaptor proteins contains only one SH2 domain,
whereas they usually possess two or more SH3
domains. In theory, more than one SH3 domains may
allow the adaptor to recruit several ligands separately;
however, it seems from earlier studies that cooperation
L. Buday and P. Tompa Functional classification of scaffold proteins
FEBS Journal 277 (2010) 4348–4355 ª 2010 The Authors Journal compilation ª 2010 FEBS 4351
exists between the SH3 domains for ligand binding. For
example, Nck adaptor contains one SH2 domain and
three SH3 domains. Although individual SH3 domains
of Nck were reported to be able to bind partners, such
as p21 protein (Cdc42 ⁄ Rac)-activated kinase or PRK2,
experimental data clearly showed that Nck constructs
containing all three SH3 domains bind the protein part-

ners with much higher affinity than the single SH3
domains [15,16]. Therefore, it is highly likely that even
those adaptors which contain two or three tandem SH3
domains actually link only two members of a catalytic
pathway.
SH2 ⁄ SH3 domain-containing adaptors link down-
stream target molecules to the membrane-bound recep-
tor. In some cases, the adaptor may recruit binding
partners directly to the plasma membrane through its
lipid-binding domain. In hematopoietic cells, pleckstrin
homology domain (PH)-containing adaptor molecules
provide important links between phosphoinositide-
3 kinase and lymphocyte function. For example,
recruitment of Src kinase-associated phosphoprotein
(SKAP) and B-lymphocyte adapter molecule of 32 kDa
(Bam32) ⁄ dual-adapter for phosphotyrosine and 3-phos-
phoinositides (DAPP) to the plasma membrane of acti-
vated lymphocytes is driven by lipid products generated
through the action of phosphoinositide-3 kinase [17].
Whereas SKAP contains a PH domain on the N-termi-
nus and an SH3 domain on the C-terminus, Bam32 ⁄
DAPP1 possesses an SH2 domain and a PH domain.
Therefore, although both adaptors could bind phospho-
inositide in the plasma membrane, SKAP recruits pro-
line-rich target molecules, whereas Bam32 ⁄ DAPP1 may
associate with phosphotyrosine-containing proteins.
Possessing a PH domain for membrane association, this
subfamily of adaptors, including SKAP, Bam32 and
SH2B proteins, performs a bona fide adaptor function,
they nevertheless link downstream targets directly to

the plasma membrane DAPP [17].
The majority of adaptor molecules are implicated in
RTK signaling, however, other cell-surface receptors
also utilize adaptors possessing specific modular
domains. Death receptors, members of the tumor
necrosis factor receptor superfamily, possess a cytoplas-
mic death domain (DD). They transmit signals through
apical protein complexes, which are nucleated by the
death domain adaptors Fas-associated protein with
death domain (FADD) and tumor necrosis factor
receptor type 1-associated death domain protein
(TRADD). FADD is a protein containing two structur-
ally similar protein motifs, the N-terminal death effec-
tor domain and the C-terminal DD. The primary role
of FADD in death receptor signaling is to recruit initia-
tor procaspase 8 and procaspase 10 to death receptors
[18]. The principle by which the SH2 ⁄ SH3 domain-con-
taining adaptors and FADD function is very similar,
and the modular domains of growth factor receptor-
bound protein 2 and FADD are commutable. This was
demonstrated by creating an artificial signaling pathway
in which the SH2 domain of growth factor receptor-
bound protein 2 was fused to the death effector domain
of FADD. The chimeric adaptor protein could reroute
RTK signals to induce procaspase activation and cell
death [19].
Classification of scaffolds and its
limitations
The functions of the above four closely related catego-
ries of signaling regulatory proteins show significant

similarities and overlap (Fig. 1 and Table 1), but
appear to segregate into three broad functional catego-
ries: simple proteins binding two partners together
(adaptors), larger multidomain proteins targeting and
regulating more proteins in complex ways (scaf-
folds ⁄ anchoring proteins) and proteins specialized to
initiate signaling cascades by localizing partners at the
cell membrane (docking proteins).
This classification has both advantages and limita-
tions. Its major advantage is simplification, because it
enables one to think in terms of a few concepts instead
of a practically unmanageable number of individual
observations. This very fact, however, also makes it
inherently limited, because of the necessary neglect of
many details. If such exceptions to the ‘rule’ of the
system become too numerous, the system has to be
improved ⁄ refined to comply with progress in the field.
Here we list a few such notable exceptions that may
eventually demand the extension of the classification
scheme.
A diagnostic mark of the limitations inherent in the
scheme is that very often the names are used inter-
changeably, without much attempt to clarify where the
given protein belongs to. For example, anchoring pro-
teins are often also termed scaffolds [4,7], the term scaf-
folds and adaptors are sometimes used interchangeably
[1,4], the distinction between docking and adaptor is
somewhat arbitrary [6], and docking proteins may also
be termed adaptors and scaffolds [2]. There are many
individual proteins called by different names in differ-

ent articles, such as MyD88 scaffold and adaptor [3],
linker for activated T cells (LAT) scaffold [3] and dock-
ing protein [6], GAB docking protein [6] and scaffold
[4], mAKAP anchor protein [7] and scaffold [4], MAG-
UK proteins, which ‘anchor’ receptors at the synapse,
scaffold [1] and adaptor [20], FGF receptor substrate
docking protein [6] and ‘scaffold adaptor’ [21]. These
Functional classification of scaffold proteins L. Buday and P. Tompa
4352 FEBS Journal 277 (2010) 4348–4355 ª 2010 The Authors Journal compilation ª 2010 FEBS
and many other examples in the literature demonstrate
that the terms cannot be unequivocally separated.
A different type of limitation is the exclusion of pro-
teins with enzymatic activity. Although it serves the
simple purpose of separating two basic functions in
signal transduction – enzymes that act and proteins
that orchestrate their action [22] – it is clear that it
cannot be done for many relevant proteins that have
both enzymatic domains and regulatory protein–pro-
tein interaction domains. In effect, there are several
proteins considered as scaffolds that have enzymatic
activity, such as MAGUK proteins already discussed
among scaffolds [3], RNAse E [23], MEKK1 of the
JNK signaling pathway [24], RTKs themselves [3] or
integrin-linked kinase [25]. Actually, there is little func-
tional distinction between a scaffold protein binding a
given enzyme partner and a scaffold that has an enzy-
matic domain of the same type.
An additional complicating factor is that there are
many other signaling pathways beyond kinase cascades,
which are rather neglected in this context. For example,

transfer of the small protein ubiquitin proceeds via a
cascade, from E1 ubiquitin-activating enzyme to E2
ubiquitin-conjugating enzyme to a specific substrate
with the intervention of a targeting-type of interaction
mediated by E3 ubiquitin ligases. Because ubiquitinated
target proteins may be targeted for degradation or sig-
naling activation [26], the operation of E3 proteins,
such as MDM2 [27] and Siah-2 [28], can be best ratio-
nalized by the scaffold concept. The assembly of Esc-
herichia coli RNA degradosome by RNAse E [23] is
also of very similar molecular logic. It has been sug-
gested that there are also adaptors that are important in
pathways activated by internal signals, such as DNA
damage, e.g. MDC1 in DNA doule-strand breaks [20]
and BRCA1 in many cellular pathways including DNA
repair [29]. In a similar vein, trafficking of signaling
proteins is itself dependent on adaptors associated with
protein sorting in endosomes, such as ESCRT [30]. In
addition, both proteins and also metabolites can be
scaffolded, as demonstrated by Pmel17, a physiological
amyloid that ‘scaffolds’ and ‘sequesters’ toxic interme-
diates during the biosynthesis of the pigment melanin in
melanocytes in the skin [31].
Of further note, many fully or largely disordered pro-
teins noted for their assembly function (see below) are
not usually considered to be scaffold proteins, although
they do bind and orchestrate the action of several sig-
naling partners, such as caldesmon (Ca
2+
⁄ calmodulin,

F-actin, myosin, tropomyosin), SIBLING proteins
(integrin, complement factor H, CD44, fibronectin), or
RNAPII CTD (capping, splicing and polyadenylation
factors). The molecular mechanism and function of
these proteins also comply with the scaffolding princi-
ples outlined in this article.
Scaffold proteins and structural
disorder
The decision on what is included among scaffolds can
also be approached from a structural point of view,
because in all categories – with the possible exception of
adaptors – the proteins have a very high level of func-
tion-related structural disorder (Table 1). It has recently
been recognized that a significant proportion of eukary-
otic genomes encodes for proteins (IDPs) or regions of
proteins (IDRs) that lack a well-defined 3D structure
under native, functional conditions [10,32–34]. Struc-
tural disorder abounds in proteins of regulatory and sig-
naling function, and it is also closely correlated with
disease, such as cancer and neurodegenerative disorders.
The molecular function of IDPs ⁄ IDRs may stem either
from recognition of partner molecules via short motifs
[35,36] or disordered domains [37], from regulatory
post-translational modification and also from providing
‘entropic-chain’ functions, such as linkers and segments
contributing entropic exclusion and force generation.
As a result, the molecular function of scaffolds corre-
sponds to the ‘assembler’ function of IDPs, i.e. they
have been described to assemble complexes [9,34,37].
The role of structural disorder in scaffold-type func-

tions is also apparent in hub proteins, which have been
found to have a large number of binding partners in
high-throughput studies of protein–protein interactions
in the interactome [38]. In particular, ‘party’ hubs have
been defined as those being able to bind their partners
simultaneously, which is the very essence of the action
of scaffolds. Hub proteins have an elevated level of dis-
order [39], which is also the case with the examples cited
here (average disorder, 43.3%; Table 1), and also previ-
ous findings that scaffold proteins constitute one of
the most disordered functional categories [8,40] and the
average disorder correlates with the number of subunits
of multiprotein complexes [41]. In all, structural disor-
der seems to be closely associated with several attributes
of scaffold function, such as the ability of binding multi-
ple partners, mediating their complex and transient
interactions and themselves undergoing a complex array
of regulatory post-translational modifications (Fig. 1).
Conclusion: where is the field of
scaffolds headed?
From all the considerations described, it seems that a
useful practical functional classification of scaffold
proteins and their kin can be given. At first sight, all
L. Buday and P. Tompa Functional classification of scaffold proteins
FEBS Journal 277 (2010) 4348–4355 ª 2010 The Authors Journal compilation ª 2010 FEBS 4353
the proteins enlisted represent variations on a common
theme, binding signaling proteins together to direct
and control the flow of information in the cell. This
basic theme segregates in a rather consistent manner
into three coherent categories. Scaffold ⁄ anchor pro-

teins usually bind more than two signaling components
together and regulate their activity in complex and
dynamic ways, involving activation and repression of
activity. Adaptor proteins are usually smaller and their
function is simpler, connecting two partners together.
Docking proteins distinguish themselves by assembling
signaling complexes at the plasma membrane in a Tyr-
phosphorylation-dependent way. There are many pro-
teins excluded from this scheme, although they do act
via very closely related mechanisms. Their inclusion
following careful judgment of their functional modes,
possibly leading to an extension of the classification
scheme, should be considered.
Acknowledgements
This work is supported by grants OTKA K60694 and
NK71582 from the Hungarian Scientific Research
Fund and ETT 245 ⁄ 2006 from the Hungarian Ministry
of Health (for PT), the Miha
´
ly Pola
´
nyi Program
(Agency for Research Fund Management and
Research Exploitation, KPI) and a ‘Lendu
¨
let’ grant
from the Hungarian Academy of Sciences (for LB).
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