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Molecular and Cellular Biology, June 2000, p. 3906-3917, Vol. 20, No. 11
0270-7306/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
Interaction between PAK and Nck: a Template for Nck
Targets and Role of PAK Autophosphorylation
Zhou-shen
Zhao,1
Edward
Manser,1,* and
Louis
Lim1,2
Glaxo-IMCB Group, Institute of Molecular & Cell Biology, Singapore 117609, Singapore,1 and
Department of Neurochemistry, Institute of Neurology,
University College London, London WC1N 1PJ, United
Kingdom2
Received 4 October 1999/Returned for modification 1 December
1999/Accepted 5 March 2000
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ABSTRACT |
The kinase PAK binds tightly to the SH3 domain of its partner PIX
via a central proline-rich sequence. A different N-terminal sequence
allows
PAK to bind an SH3 domain of the adaptor Nck. The Nck
SH3[2] domain interacts equally with an 18-mer PAK-derived peptide
and full-length
PAK. Detailed analysis of this binding by saturation
substitution allows related Nck targets to be accurately identified
from sequence characteristics alone. All Nck SH3[2] binding proteins,
including PAK, NIK, synaptojanin, PRK2, and WIP, possess the motif
PXXPXRXXS; in the case of PAK, serine phosphorylation at this site
negatively regulates binding. We show that kinase autophosphorylation
blocks binding by both Nck and PIX to
PAK, thus providing a
mechanism to regulate PAK interactions with its SH3-containing
partners. One cellular consequence of the regulatable binding of PAK is
facilitation of its cycling between cytosolic and focal complex sites.
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INTRODUCTION |
Signal transduction pathways often
utilize protein-protein interaction modules whose domain structures are
conserved at the primary or secondary structural level. Two domains
frequently found on signaling molecules are Src homology 2 and 3 domains (41). In Src, these domains not only regulate
association with other proteins but also intramolecular functions,
including protein tyrosine kinase activity (35). The adaptor
signaling molecules contain no catalytic domain (41).
The best studied of these is Grb2, whose SH3 domains complex to
the Ras guanine nucleotide exchange factor (GEF) SOS. Upon
stimulation, tyrosine kinase receptors that engage Grb2 through binding
to its SH2 domains recruit the Grb2-SOS complex, thus causing Ras
activation (7).
We have recently described a new class of Rac1 GEF whose SH3 domain
binds selectively to a nonconventional proline-rich binding sequence
present in all mammalian PAKs (32). Because these
PAK-interacting exchange (PIX) proteins are complexed to PAK, the
kinase has roles both upstream and downstream of Rac and/or Cdc42
(39). Thus, recruitment of the complex via PAK leads to Rac
activation, while PIX itself is known to play a role in localizing PAK
to focal complexes (FCs) and activating the kinase (32).
Although Cdc42 or Rac directly activate PAKs, the ubiquitous adaptor
protein Nck, which binds to an N-terminally located proline-rich
sequence (2, 5, 14), can also activate PAK by recruitment to
the plasma membrane (27). PAK activation by Nck is mimicked
when membrane-localizing signals are directly attached to PAK
(30). Nck contains three tandem SH3 domains and a
C-terminally located SH2 domain (8, 9, 25). The
Drosophila Nck homologue, Dock, plays a role in axonal
guidance: both DPak and Dock are highly expressed in the nervous system
(15, 18). Membrane-tethered DPak acts as a dominant
gain-of-function protein in dock mutants, restoring the
normal pattern of R-cell connectivity; thus, DPak is a key downstream
partner of Dock (19).
The structures of many SH3 domains have been determined by
crystallographic and nuclear magnetic resonance protocols. These analyses reveal that the conserved aromatic residues form a hydrophobic patch on the surface of the SH3 domain (6, 20). Part of the binding affinity is contributed by hydrophobic interactions with conserved prolines, but it also involves ionic interactions,
particularly with a basic residue positioned before or after the PXXP
motif. The position of this basic residue determines the orientation (plus or minus) of the pseudosymmetric PXXP-containing ligand on the
SH3 domain (13, 26). Since peptide binding requires the
central portion of a polypeptide to adopt a type II polyproline helix
conformation, the contexts of these target sequences play an important
role in determining the relative affinity. Thus, it has been reported
that the tight binding between Grb2 and the C-terminal region of SOS,
with affinity in the submicromolar range, requires integrity of the SOS
domain (47), whereas binding of SH3 domains to peptides
derived from their target sequences occurs with affinities in the
micromolar range (24).
In this study, we initially assessed SH3 binding of a number of
domains related to PIX SH3 using a novel SH3 overlay protocol; stable
complexes were detected with some, but not all, SH3 domains tested.
Using the second SH3 domain (SH3[2]) of Nck, direct SH3 targets
were then purified and identified by protein microsequencing. Of these,
we chose PAK and NIK for further study, identifying 18-residue peptides
within each that fulfill the binding function. Most of the identified
targets contain related proline (and serine-threonine)-rich motifs. The
interaction between Nck SH3[2] and PAK was also found to be
negatively regulated by phosphorylation in vitro and in vivo. We
propose that phosphorylation-mediated regulation of SH3 binding can
play an important role in signaling through such adapter proteins. In
the case of PAK, it appears that this effect, which occurs with both
Nck and PIX, allows the kinase to cycle between FCs and the cytoplasm.
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MATERIALS AND METHODS |
Bacterial expression vectors.
The pGEX-Ras vector was
derived from pGEX-4T-1 as follows. The Ras(1-185) coding sequence was
PCR amplified (Vent; New England Biolabs) to include a BglII
site adjacent to codon 1 and, at the 3' end (adjacent to codon 185), a
BamHI-EcoRI linker (GGATCCCCGAATTC). This fragment was cloned into the pGEX-4T
BamHI/EcoRI site, thereby regenerating a
BamHI site downstream of the Ras sequence (the original
BamHI site was lost; the new polylinker is identical to that
in pGEX-4T-3). Various SH3 domains used in this study were derived by
PCR with primers containing 5' BamHI and 3' XhoI cloning sites. The amplified human cDNA SH3 corresponds to the following codons (GenBank numbers are in parentheses): cortactin (A48063), 491 to 550; phospholipase C
(G4505869), 790 to 852; myosin
1C (U14391), 1052 to 1109; Nck SH3[1], 1 to 98; Nck SH3[2], 110 to
176; and Nck SH3[3], 167 to 266. The construct containing Nck
SH3[1,2,3] contained residues 1 to 266.
PAK(1-250) is derived
from a BamHI/BglII fragment as described
previously (30). The
PIX SH3 domain was described
previously (32).
Constructs encoding peptide sequences were derived from synthetic
oligonucleotides containing the appropriate overhangs which were cloned
into the BamHI and XhoI sites of pGEX 4T-1. (See
Fig. 3 for the sequences of these peptides [which also contained 3' termination codons].) The PTP-PEST sequence (328 to 344) encoded SKQDSPPPKPPRTRSCLV. Plasmids encoding the
glutathione-S-transferase (GST) or GST-Ras fusion proteins
were transformed into the Escherichia coli BL21 strain for
protein expression as described previously (30).
Mammalian expression vectors.
The pXJ-HA and pXJ-Flag
mammalian vectors used for transfection and microinjection experiments
have been described previously (30). The full-length Nck
sequence was amplified with oligonucleotides containing 5'
BamHI and 3' XhoI sites. Full-length rat GIT1
(42) was derived from a cDNA library and cloned, also using
a BamHI site flanking the initiator methionine.
Purification of Nck binding proteins.
GST-Nck SH3[2]
proteins were dialyzed overnight against phosphate-buffered saline
(PBS) and coupled to cyanogen bromide (CNBr)-activated Sepharose
(Sigma) to yield 2 mg of affinity matrix/ml. Rat tissues were
homogenized in buffer A (25 mM HEPES [pH 7.3], 0.5% Triton X-100, 1 mM EDTA, 25 mM NaF, 1 mM sodium orthovanadate), freshly added 5 mM
dithiothreitol, and 10 µg each of leupeptin and aprotinin/ml. The
supernatants from centrifugation (100,000 × g; 40 min)
were diluted to 5 mg/ml with buffer B (PBS plus 50 mM Tris-HCl, pH 7.8, 0.1% Triton X-100, 0.5 mM MgCl2) and passed through
affinity columns (a ratio of 20 ml of extract per ml of matrix). After washing with 10 column volumes of buffer B, bound proteins were released by heating them (100°C; 10 min) in a 1/5 dilution of sodium
dodecyl sulfate (SDS) sample buffer (0.4% SDS) and concentrated. Sepharose Q (Pharmacia) ion-exchange chromatography was carried out
manually using a ratio of 20 mg of brain extract/ml of Sepharose. After
the sample was loaded, elution was carried out in buffer A containing
100 mM incremental NaCl steps (up to 500 mM). The 150 to 350 mM
fraction was collected by washing it with 2 column volumes of 150 mM
NaCl buffer and eluting with 2 column volumes of 350 mM buffer. This
fraction was immediately loaded onto a 1-ml Nck SH3[2]-Sepharose
column, washed, and processed as described above. The relevant bands
were excised from the stained gels and processed for protein
microsequencing as described previously (30).
Overlays with [
-32P]GTP labeled proteins.
The Pepspot filter and the PAK9-23 and
PAK9-23(PS21) phosphopeptides were synthesized and purified
by Jerini Biotools. The purified proteins were separated on 10%
SDS-polyacrylamide gels and transferred to polyvinylidene difluoride
(PVDF) (NEN) membranes. The filters were blocked for 2 to 16 h
(4°C) in PBS containing 10% skim milk prior to overlay analysis. The
GST-Ras fusion proteins (10 µg) were incubated for 4 min with 10 µCi of [
-32P]GTP in 50 µl of exchange buffer (25 mM HEPES [pH 7.3], 50 mM KCl, 2.5 mM EDTA). This mixture was
immediately added to 3 ml of binding and wash buffer (PBS containing 25 mM HEPES, pH 7.3, 5 mM MgCl2, and 0.05% Triton X-100)
containing 0.1 mM GTP and added to a roller bottle containing the PVDF
membrane. Following a 1-h incubation at 4°C, the filters were washed
(three times for 10 min each time) with binding and wash buffer and
exposed to PhosphorImager plates (Molecular Dynamics) for
quantification or to X-ray film.
Biacore analysis.
The Nck SH3[2] domain was cloned into
the pMal vector (New England Biolabs) in order to express
maltose-binding protein (MBP) fusions. Proteins were eluted from the
amylose resin in PBS containing 50 mM Tris-HCl, 5% glycerol, 0.1%
Triton X-100, 0.5 mM MgCl2, and 20 mM maltose and stored at
70°C prior to use. For Biacore studies, the GST-PAK or GST-peptide
proteins were dialyzed overnight against PBS and coupled to CM5 sensor
chips (Pharmacia-LKB) under standard immobilization conditions in 10 mM
sodium acetate (pH 5.0). The sensorgrams were collected at 10-µl/min
flow rates at 24°C using Pharmacia HEPES-buffered saline (HBS)
buffer-0.05% NP-40. Regeneration cycles were carried out by treating
the surface with HBS plus 0.1% SDS for 4 min.
Cell microinjection, transfection, and staining.
Subconfluent HeLa cells were microinjected into the nucleus with 50 ng
of each expression plasmid DNA/ml using an Eppendorf microinjector.
After 2 h, the cells were fixed in 3% paraformaldehyde for 20 min
and stained as described previously (30). COS-7 cells were
transfected using 3 µg of plasmid plus 30 µl of DOSPER (Roche) per
100-mm-diameter dish and harvested 16 h after the addition of DNA.
Antibody sources were as follows: anti-Flag and anti-Flag M2 Sepharose
were from Sigma, anti-hemagglutinin was from Roche, anti-paxillin was
from Transduction Laboratories, and anti-
PAK was as described
previously (30).
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RESULTS |
A subset of SH3 domains identifies target proteins in
overlays.
PIX binds with high affinity to PAK-derived peptides
(32) and overlays by using the PIX SH3 domain to selectively
detect PAKs (i.e., the bona fide targets). This prompted us to
determine whether related SH3 domains exhibited similar properties. The ligand overlay method has been used in the analysis of SH3 binding (45, 54) and is most sensitive when
-32P-labeled SH3 probes are employed. To facilitate
rapid and efficient labeling of fusion proteins, we have exploited the
ability of the small G protein Ras to rapidly sequester
[
-32P]GTP in an Mg2+-dependent
manner with a Kd of ~10
12. The
GST-Ras-SH3 fusion system shown in Fig.
1A allows efficient (>90%)
incorporation; this contrasts with labeling methods such as the use of
kinase phosphorylation with [
-32P]ATP, which in our
hands is ~10% efficient. GST-Ras itself does not produce
signals after proteins are subjected to SDS-polyacrylamide gel
electrophoresis (Fig. 1B). We then probed rat tissue extracts for
binding proteins using the SH3 domains of
PIX, phospholipase C
(PLC
), myosin 1C, cortactin, and Nck (designated [1], [2], and
[3]). Interestingly those SH3 domains more closely related to PIX
(32) formed stable complexes with specific proteins enriched in brain and testis (Fig. 1). The patterns of binding proteins detected with myosin 1C, PLC
, and Nck[2] SH3 domains were
distinct. The ~100-kDa brain protein detected by most probes
corresponds to dynamin, which binds many SH3 domains in vitro
(16).

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FIG. 1.
Protein overlays define multiple target proteins for
certain SH3 domains. (A) Schematic diagram of the GST-Ras construct
showing the arrangements of structural domains.
[ -32P]GTP (asterisk) is introduced into the fusion
protein by incubating the protein for 4 min in buffer containing 2.5 mM
EDTA. Binding and washes are performed in buffers containing 5 mM
MgCl2. (B) Labeled SH3 domains as shown were overlaid onto
blots (on PVDF) containing 80 µg of soluble proteins derived from rat
tissues: brain (B), testis (Te), and heart (H). The filters were
exposed for 4 h at 70°C. As a control, GST-Ras alone produces
no signals. In addition to dynamin (~100-kDa band in brain), the
PIX SH3 domain detects the three isoforms of PAK ( , , and
), with the level of PAK being highest.
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Nck SH3[2] was selected for further study, since among its binding
partners are the serine and threonine PAK kinases that
are targets for
Cdc42 and Rac1 (
31). The Nck SH3[1,2,3] binding
pattern
indicated that no further targets were detected (not shown),
suggesting
these flanking SH3[1] and SH3[3] domains do not add
significantly
to binding stability under these assay conditions.
To establish the
identities of the other proteins that also bind
robustly to Nck
SH3[2], we then undertook purification of these
proteins from rat
brain.
Purification and microsequencing of Nck SH3[2] binding
proteins.
GST-SH3 affinity chromatography has been used to purify
and identify many target proteins. Using total cytosolic extracts, numerous bands were eluted (compared with GST alone), although only a
subset of these represent direct targets for Nck SH3[2] (Fig.
2A). This confirmed that proteins
detected in overlays do interact in solution; only the ~100-kDa brain
protein (dynamin) was sufficiently pure for identification.
Ion-exchange fractionation prior to affinity chromatography reduced
nonspecific components (compare Fig. 2A and C), with the fractions
monitored by SH3 overlay (Fig. 2B). The p140 and p160 bands were
clearly separated under these conditions. The relative intensity of the
p60 band increased during purification, possibly due to proteolysis of
the p68 band (see Discussion). The Q-Sepharose brain fraction (150 to
350 mM NaCl fraction), depleted of dynamin, was applied to a 1-ml Nck SH3[2]-CNBr Sepharose column, and SDS-released material was separated on a 7.5% polyacrylamide gel. Sufficient protein was obtained for
conventional tryptic peptide microsequencing. Corresponding peptide
sequences matched the proteins shown in Fig. 2C. Of these, p145
synaptojanin had not previously been identified as a Nck partner. From
comparison of signals obtained by overlays with their Coomassie
blue-stained counterparts, we conclude that in brain extracts NIK,
synaptojanin, and the p68s (SAM68, N-WASP, and PAK) bind most tightly.

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FIG. 2.
Purification of Nck binding proteins. (A) Detection of
binding proteins from brain (B) and testis (Te) extracts. Total
cytosolic extracts were passed through columns containing immobilized
GST or GST-Nck SH3[2] as indicated. Proteins eluted with SDS
treatment (left) were analyzed by GST-Ras-Nck SH3[2] binding.
Differences between brain and testis samples are the p140 brain and the
testis p110 binders. Numbers on the left are the molecular masses (in
kilodaltons) of the markers, and those on the right indicate the
positions of the six Nck binding proteins. (B) Sepharose Q ion-exchange
fractionation of brain proteins was carried out as described in
Materials and Methods. T, total extract; FT, flowthrough fraction; W,
wash fraction; HS, high-salt fraction. The Nck SH3[2] binding
proteins were assayed using 20 µl of material from each fraction. (C)
Identification of Nck binding proteins by protein microsequencing.
Bands were excised from the Coomassie blue-stained gels as shown and
processed for tryptic digestion, high-performance liquid chromatography
separation, and Edman microsequencing. At least three peptides with
unambiguous sequences were used to identify the proteins as shown.
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Sequence requirement for efficient Nck SH3[2] binding.
The
smallest region of NIK previously shown by yeast two-hybrid analysis to
bind Nck encompassed residues 443 to 620, which contains two
proline-rich regions apparently involved in binding Nck
(53). We expressed these sequences individually as
18-amino-acid peptides fused to GST (Fig.
3A) and tested them by overlay for binding to Nck SH3[2] (Fig. 3B). NIK18-2 resembles the proline-rich sequence PAK18-1 (Fig. 3A) that binds Nck SH3[2] (49), and
both contain the PXXPXRXXS consensus sequence previously derived for Nck SH3[2] (43). Interestingly, PAK18-1 binds as
efficiently as full-length PAK (Fig. 3C), suggesting that its binding
was not further stabilized by the peptide being present within a larger domain. A smaller, 13-residue peptide, PAK13, also bound Nck SH3[2], albeit with fourfold-reduced signal (Fig. 3C); thus, the five residues
N terminal to PAK13, though not essential, do contribute to binding.
Significantly, PAK13m, in which an acidic residue replaces
S21, gave no signal.

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FIG. 3.
Identification of the Nck binding region in NIK and PAK.
(A) Peptide sequences used to test Nck SH3[2] binding as indicated
were expressed as GST fusion proteins. Residues conserved between PAK
and NIK are in boldface; the arrowheads indicate the position of
phosphorylated serine in PAK or nontolerated residues in NIK18 1. There
is a phosphorylated serine in the Plx binding site (asterisk). (B) GST
proteins displaying peptides (1 or 2) derived from PAK and NIK in panel
A were analyzed by Nck SH3[2] overlay following separation of 2 µg
of each protein on a 10% polyacrylamide gel. (C) PAK18 binds with
efficiency similar to that of full-length PAK. A comparison of binding
to 2 µg of PAK(L404S) or 1 µg of the various peptides
indicated in panel A is shown. The smaller peptide, PAK13, binds more
weakly than PAK18; in this context, PAK13S21E fails to bind Nck.
Numbers on the left indicate the molecular masses (in kilodaltons) of
the markers.
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Stable complexes between Nck SH3[2] and target peptides in
vitro.
To directly assess the binding of Nck SH3[2] to target
sequences, we next used surface plasmon resonance analysis. Since the dimerization behavior of GST fusion proteins in solution can contribute to spurious Biacore measurements (21), Nck SH3[2] was
purified as a fusion with MBP. The relative sizes of these
proteins were determined by gel filtration (Fig.
4A). The MBP-SH3 protein behaved as a
monomer under these conditions. This fusion protein was then tested against GST-PAK, GST-PAK1-250, and GST-PAK18
immobilized to the biosensor chip (approximately equal mass coupling).
The trace shows binding at 1 µM MBP-Nck SH3[2], which exhibits
biphasic kinetics (Fig. 4B). Considering the coupling efficiency and
molecular mass differences, the extents and rates of binding were
essentially identical. The binding showed a component with an unusually
slow dissociation phase. Similar results were obtained with NIK18 (data
not shown).

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FIG. 4.
Biacore analysis of the interaction of SH3 domains with
target sequences. (A) Superdex200 gel filtration analysis of
GST-SrcSH3. The thrombin-cleaved material (dotted line) was treated
with 10 U of thrombin per ml for 1 h at room temperature to
release free SH3. The GST proteins are present exclusively as dimers,
while MBP-Nck SH3[2] exhibits retention corresponding to a monomeric
~50-kDa protein. Analytical gel filtration was conducted on the Smart
system (Pharmacia) in HBS at 30 µl/min at 20°C. Standard protein
markers (Sigma) are indicated by arrowheads: lysozyme, 14 kDa; carbonic
anhydrase, 29 kDa; serum albumin, 66 kDa; and alcohol dehydrogenase 150 kDa. (B) Coupling (rU values) to CM5 channels was as follows: control
channel GST, 2,110; GST-PAK18, 1,650; GST-PAK1-250, 1,760; and
GST-PAKL404S, 2,280. The sensorgram shows the addition of 1 µM
MBP-Nck SH3[2] at a flow rate of 10 µl/min.
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Substitution analysis of PAK(11-23) binding to Nck
SH3[2].
All 260 peptides corresponding to the core binding
sequence (PAK13) and containing every possible single-point
substitution were synthesized on cellulose and assayed by Nck SH3[2]
overlay (Fig. 5A). This
analysis reveals both preferred residues and nontolerated substitutions
and is more informative than alanine scanning substitution. Following a
10-min exposure to the storage screen, spot values were quantified:
wild-type peptide sequences yielded (7.2 ± 1.4) × 106 U (n = 13). Residues producing the
strongest binding (i.e., preferred) or values of <1 × 106 at a given position are presented in Fig. 5B. The
requirement for prolines (particularly P13 and P16) within the sequence
is not unexpected, but two novel aspects were noted. First, the
conserved R18 is absolutely required for binding (K18 is not accepted). Second, C-terminal to this arginine, neither proline nor acidic residues are tolerated, suggesting that both structure and charge can
regulate binding. The fact that serine is clearly preferred by
Nck SH3[2] at
PAK21 has already been noted
(43). The PAK18-1 (wild-type) sequence is optimal for Nck
binding at most positions: stronger binding by NIK18-2 than by PAK18-1
can be attributed to an arginine in the position equivalent to PAK M22
(Fig. 3A). The failure of NIK18-1 (DPCPPSRSEGL) to bind Nck (Fig. 3B)
is related to poorly tolerated residues (underlined). Within
the
PAK sequence, S21 is known to be autophosphorylated
(30); substitution by acidic residues completely blocks
binding (also see Fig. 3C).

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FIG. 5.
Positional residue preferences for peptide
binding to Nck SH3[2]. (A) Synthetic peptides corresponding to the
PAK Nck binding sequence (indicated on the left and marked
by white crosses) and containing all possible point substitutions (260 peptides) were synthesized in an array. The filter was blocked with 1%
bovine serum albumin and probed with 32P-labeled Nck
SH3[2] under standard conditions. A 10-min exposure is shown. (B)
From phosphorimager analysis of panel A, preferred (highest counts) or
required (boldface) and poorly tolerated (<20% of wild type) peptides
are tabulated. Note that the presence of proline or acid residues in
the C-terminal half of the peptide drastically reduces binding. (C)
Identification of putative binding sequences in known Nck targets.
Mammalian proteins identified by PHI-Blast (58) using the
PAK 13 sequence and the motif P-X-[AIKLPRTV]-P-X-R-[exclude
DEP]-[exclude DEP]-S. Matches were found in all targets that had
previously been shown to directly bind Nck (asterisks), while
other proteins with the potential to bind Nck are also shown. The
conserved residues are highlighted in boldface. (D) Nck SH3[2] can
bind to the proline-rich region of PTP-PEST (328 to 344); as a positive
control, the NIK18 peptide (2 µg) was corun on a 10% polyacrylamide
gel and analyzed by overlay for binding). Asterisks represent sites
where only 1 residue is tolerated.
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Nck SH3[2] binding proteins are identified from sequence
analysis.
Other than PAKs, only the tyrosine kinase Arg has an Nck
binding site (residues 659 to 671), which has been precisely mapped (55) and which we now predict binds via SH3[2]. The motif
PXXPXRXXS, but conforming to the PAK peptide-based consensus, was
detected in many Nck partners (aligned in Fig. 5C), including
synaptojanin 1, Nck-associated protein 4 (NAP4) and NAP5
(34), PRK2 (43), and WASP-interacting protein
(WIP). Novel candidate binders were detected by PHI-Blast
(58), including the phosphatidylinositol polyphosphate-5-phosphatase SHIP2, the p60 IRS-3, the p150 c-Abl, and members of the PTP-PEST tyrosine phosphatase family.
Interestingly, a Drosophila protein, dPTP61F, is a potential
partner for the Drosophila Nck homologue (10) and
contains a consensus binding site for Nck SH3[2]; no direct
mammalian dPTP61F homologue is known.
We were interested in the possibility that p110 (Fig.
1; also see Fig.
7) might correspond to proteins of the PTP-PEST family
which associate
with FCs through paxillin (
51). When tested,
the
proline-rich sequence derived from PTP-PEST indeed bound Nck
SH3[2]
as avidly as did NIK18 (Fig.
5D). Thus, it is likely that
the proteins
listed in Fig.
5C indeed have the potential to bind
Nck.
PAK autophosphorylation regulates Nck binding.
Since certain
substitutions by acid residues (Fig. 5A) were deleterious to PAK
binding, this suggested that phosphorylation within these sequences
might provide a mechanism to regulate such binding. Indeed, purified
COS-7-derived recombinant
PAK loses its ability to bind Nck SH3[2]
upon activation by GTP
S-Cdc42 in an ATP-dependent manner (Fig.
6A). Similarly, recombinant
(autophosphorylated) GST-PAKL107F did not bind to Nck. The disruptive
effect of phosphorylation on the PAK-Nck complex was also borne out by
in vivo analysis. Complexes between PAK and Nck occur in cultured
cells (14), and also when they are coexpressed (Fig. 6B).
The expression of Cdc42G12V with PAK (and Nck) leads to
kinase activation (as detected by an upward shift in mobility), but Nck
immunoprecipitates no longer contain PAK (Fig. 6B, lane 2).
Cdc42G12V does not promote dissociation of the PAK-Nck
complex with the catalytically inactive
PAKK298A (lane
3), showing that the effect is indeed mediated through autophosphorylation. Thus, within cells it seems likely that following recruitment by GTP-Cdc42 or GTP-Rac1, PAK-Nck complexes dissociate upon
PAK activation.

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FIG. 6.
Phosphorylation of PAK regulates Nck binding.
(A) Effect of Cdc42-mediated activation of PAK on Nck SH3[2] binding.
The top gel shows Coomassie blue-stained COS-7-expressed Flag- PAK
immunoprecipitated and incubated (30 min; 30°C) in the presence (+)
of 2 µg of recombinant Cdc42 with (+) 0.1 mM GTP S or GDP and/or
0.2 mM ATP as indicated. Neither Cdc42-activated PAK nor
intrinsically active recombinant GST- PAKL107F binds Nck. As a
control, the unphosphorylated GST- PAKL404S (1 µg) bound normally.
(B) PAK activation in vivo leads to dissociation of PAK and Nck.
COS-7 cells were transfected with 3 µg of the constructs per
100-mm-diameter plate as shown. The expression of PAK is shown in
the lower gel. Flag-Nck immunoprecipitates contain PAK as expected,
but not when the kinase is activated. As a control, kinase-dead (KD)
PAK(K298A) was found to be equally associated with Nck even with
Cdc42G12V present. Wt, wild type. (C) Phosphorylation of
S21 blocks Nck binding. Increasing concentrations (micromolar) of
synthetic peptides corresponding to PAK9-23 or its
phospho-S21 counterpart were coincubated with the Nck-SH3[2] probe.
Each lane of the upper gel corresponds to a strip of filter incubated
separately with the probe. The phosphorylated variant was unable to
compete for binding to the GST-PAK1-250 target (0.5 µg
per lane).
|
|
In peptides derived from the N terminus of

PAK, S21 is not
phosphorylated by exogenous active PAK (data not shown), but this
represents an intramolecular phosphorylation site in

PAK
(
30).
We therefore tested the notion that S21
phosphorylation plays
a key role by using a synthetic
PAK
9-23 peptide and its S21-phosphorylated counterpart to
compete with
Nck SH3[2] probe for binding to immobilized
GST-PAK
1-250 (Fig.
6C). Over the concentration range tested
(10 to 100 µM),
synthetic PAK
9-23 peptide, but not the
phosphorylated version of the peptide, was
effective as a
competitor.
Is phosphorylation widely used as a regulator of SH3
interactions?
Since all of the Nck binding sites we identified
(Fig. 5C) have the potential for regulation by phosphorylation, we were
interested in determining which of them might exhibit such an effect in
vivo. Figure 7A, left, shows that similar
Nck targets exist in cultured cells. We therefore briefly treated HeLa
cells with okadaic acid (inhibiting serine-threonine phosphatase
activity) and tested total lysates by overlay for Nck binding. The p50
and p160 (NIK) bands were clearly reduced by such treatment (a
representative result is shown in Fig. 7A). The p68 band was neither
reduced nor shifted, indicating that PAK was not activated under these conditions. This method has the potential to rapidly detect regulatable SH3 interactions but does not identify all such events.

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|
FIG. 7.
Identifying Nck and PAK interactions that are negatively
regulated by phosphorylation. (A) Nck SH3[2] binding proteins
detected in total proteins (80 µg/lane) from cultured cells are
compared to those in brain extract. The sizes of the various targets
are indicated; of these, p160 is suggested to represent NIK and p68 is
suggested to represent PAK. The identities of the relatively
abundant p110 and p50 species are unclear. The right gel shows reduced
Nck SH3[2] binding to HeLa cell extracts following 100 nM okadaic
acid treatment (30 min) to induce general phosphorylation. Proteins
with mobilities corresponding to 110 and 68 kDa showed no change;
however, the p160, p60, and p58 bands showed significant loss of
binding. These data are representative of two experiments. (B)
Immunoprecipitated PAK was activated in vitro with GTP S-Cdc42 and
probed with Ras-PIX SH3. Loss of binding correlated with
autophosphorylation. The GST- PAK175-206 PIX-binding
peptide (2 µg) was incubated with active recombinant PAK (0.4 µg) plus 0.5 mM ATP (1 h; 30°C). The complete phosphorylation of
S198 and S203 is indicated by its shifted mobility (phosphoprotein
[pp]). The PIX SH3 overlay shows a decrease in binding due to this
phosphorylation. (C) PAK binding to PIX-GIT1 is negatively regulated by
kinase activation. COS-7 cells were transfected with combinations of
expression plasmids as shown. The right gels show each of the proteins
detected in total lysates (80 µg); the left gels show proteins
associating with the expressed GST-GIT1. PAK activation by
Cdc42G12V is accompanied by a mobility shift and loss of
binding. +, present; , absent.
|
|
Interestingly, activation of

PAK also substantially reduces PIX SH3
binding (Fig.
7B). Since the PIX-binding peptide

PAK
175-206 is phosphorylated by exogenous PAK, we could
demonstrate that
it is the phosphorylation of
GST-PAK
175-206 (as monitored by mobility shift after
incubation with the kinase)
that is responsible for the loss of PIX
binding, which was similar
to autophosphorylated full-length

PAK
(Fig.
7B, left). Within
the peptide, the only two serines (S198 and
S203) are known PAK
autophosphorylation sites (
30). We then
investigated the interaction
of PAK and PIX during kinase activation in
vivo. To more faithfully
replicate the cellular context, we also
introduced GIT1 (
4,
42), which we find to be constitutively
bound to

PIX and phosphorylated
by PAK (data not shown).

PAK
associated with GIT1 in a

PIX-dependent
manner when relevant
combinations were expressed in COS-7 cells
(Fig.
7C). However, in cells
expressing Cdc42
G12V (lane 5), only a small fraction
of the autophosphorylated PAK
was found associated with the
complex, though there was no change
in the binding of PIX to
GIT1.
FC targeting of PAK is under dynamic regulation.
We previously
demonstrated that PAK binding to PIX is necessary but not sufficient
for localization to FCs (32). Taking this together with our
observations that both Nck and PIX binding are negatively regulated by
phosphorylation, we considered a model in which activation of PAK
prevents its constitutive association with FCs, resulting in dynamic
equilibrium between the bound and cytosolic states (Fig.
8). Since PAK associates poorly
with the RhoA-type FCs found in resting cells, we tested this notion by transfecting a PAK kinase inhibitor domain, KID
(PAK83-149), into NIH3T3 cells and then localized the
endogenous
PAK, which indeed became associated with FCs (Fig.
9A). By contrast, the inactive mutant
KIDm(L107F)-expressing cells showed normal perinuclear PAK staining.
Similarly, when we introduced Flag-
PAK into HeLa cells (Fig.
9B, image 1), the kinase inhibitor caused a shift in equilibrium
towards FCs (image 2). Interestingly Flag-
N22
PAK, lacking the Nck
binding sequence, failed to efficiently bind FCs when cotransfected
with KID (image 3). Taken together, these results explain previous
observations that N-terminal PAK1-250, but not the
wild-type kinase, is targeted to RhoA-type FCs (30).

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FIG. 8.
PAK undergoes dynamic regulation of its interactions.
PAK is capable of forming complexes with Nck and PIX through distinct
proline-rich sequences. The kinase can be recruited to juxtamembrane
sites either through the interaction of Nck with various
tyrosine-phosphorylated receptors or by the interaction of PIX with
elements of FCs. Activation of PAK requires autophosphorylation and
causes FC disassembly; however, the kinase also loses affinity for its
partners, resulting in PAK cycling back to the cytosol.
|
|

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FIG. 9.
Regulation of PAK association with FCs. (A) Inhibition
of PAK leads to an accumulation of PAK in focal adhesions. NIH 3T3
cells were transfected with KID PAK83-149 and stained with
anti- PAK and anti-vinculin. Only in cells expressing the inhibitor
was there clear colocalization of PAK with the underlying focal
adhesions. The inactive KID(L107F) mutant (KIDm) was used as a control.
(B) HeLa cells were transfected (stars) as follows: Flag- PAK (image
1), Flag- PAK plus GST-KID (59) (image 2), and
Flag- N22 PAK plus GST-KID (image 3). Immunofluorescent detection
of rabbit anti-Flag (Upstate Biotechnology Inc.) and mouse
anti-vinculin was then performed. With inhibitor, the PAK robustly
stained vinculin-rich FCs, but PAK lacking the first 22 residues (i.e.,
the Nck binding site) was poorly localized to these structures. Bar, 10 µm.
|
|
 |
DISCUSSION |
The molecular basis of SH3 binding interactions.
SH3 domains
occur in at least 87 distinct human proteins (48). Since the
report of a 3BP-1 proline-rich sequence as the target for the Abl-SH3
domain (9), numerous proline-rich binding partners for SH3
domains have been described, all containing at their cores the binding
motif PXXP (41). The only known naturally occurring
exception is the central PIX SH3 binding sequence (PPPVIAPRPEHTKS) in
PAK and
PAK (3, 32). On the C-terminal site of this motif, the S198 is an autophosphorylation site that in this study we
show to negatively regulate binding.
The structures of several SH3-peptide complexes have been available for
some time (
56,
57), but the role of determinants
outside of
the core sequence is less well understood. Src, Fyn,
and Yes SH3
domain-selected type II peptides display absolute
specificity for
asparagine at the +1 position adjacent to the
conserved arginine
(
46). For Hck-SH3 binding to human immunodeficiency
virus
type 1 Nef, important contacts are provided by the RT loop
of the SH3
domain, increasing both the specificity and affinity
of binding
(
23). The ability of Nef to bind Hck-SH3, but not
the
related Fyn-SH3, is apparently determined by a single isoleucine
within
this loop (
22). A more recent study indicates that residues
within the RT loop reorient to form an "induced fit" with the
PXXP
flanking a helical region of Nef (
1). This may be the
basis
for the slow kinetics of tight binding that we observe with
Nck
SH3[2]. It is also possible that the S- or T-rich C-terminal
region
in Nck SH3[2] binding sequences (cf. PAK18) needs to adopt
a helical
conformation, which would explain why proline substitution
blocks
binding (Fig.
5A).
The Nck SH3[2] domain engages selectively.
The adaptor
proteins of the Grb2, Crk, and Nck families, which contain only SH2 and
SH3 domains, play pivotal roles in many signal transduction cascades
(41) and perhaps for this reason can interact with multiple
SH3 targets. The best studied of these is Grb2, which was first
identified as associating with Sos1 (and -2) via interactions of both
SH3 domains, although the N-terminal domain contribution is more
important. Affinity may not be the primary issue, since it has been
demonstrated that small peptides containing N-substituted residues at
positions normally occupied by prolines can yield Grb2 SH3 ligands with
much higher affinities (Kd up to 40 nM, some 100 times that of the natural Sos-derived 12-mer peptide) (38).
The Nck SH3[2] domain achieves selectivity in its choice of targets
through particular interactions C-terminal to the PXXP
motif. Because
neither proline or acidic residues are tolerated
in these C-terminal
positions, this serves to seriously limit
the availability of targets.
Many "proline-rich" sequences in
the database containing PXXPXRXXS
motifs also contain proline
or acidic residues at inappropriate
positions. By contrast, the
conserved sites in the PTP-PEST family
phosphatases which are
recognized by the Csk SH3 domain include acidic
and proline residues
(underlined) in corresponding positions
(
PPL
PE
RT
PESFIV)
that
facilitate binding (
17).
Identifying biologically relevant Nck SH3 partners.
The
prototype target for the Abl SH3 domain (9) was identified
by ligand overlay expression screening, which has been used successfully in many subsequent studies (33, 36, 43). One drawback is that many SH3 domains bind to the same proteins in vitro,
for example, SH3 domains from p85
, PLC
, c-Src, fgr, Grb2, and fyn
(~50% of those tested) all bind dynamin robustly (16), although it is unlikely that they all regulate dynamin function. One approach is to consider the strength of interaction: it is likely
that there is in vivo competition for SH3 binding among a variety of
potential partners. Synthetic libraries have therefore been screened to
define the optimal binding sequence with a view to identifying these
sequences in target proteins. For example, using the cortactin SH3
domain, a PPXPXKP consensus was derived (52). This motif is
indeed present in known cortactin targets, 180-kDa CortBP1
(12) and the recently described CBP90 (40), which probably corresponds to 80- and 85-kDa binding proteins detected
in brain extracts (Fig. 1B).
Partners for Nck experimentally identified in our study include NIK,
synaptojanin-1, PTP-PEST,

PAK,

PAK, and hnRNP-K. Of
these,
synaptojanin, PTP-PEST, and hnRNP-K have not previously
been reported
to bind Nck. Synaptojanin is an inositol 5'-phosphatase
present in
nerve terminals (
36), which is interesting in view
of the
roles of
Drosophila Nck and Dock in axonal guidance. The
more ubiquitous synaptojanin-2 does not contain a Nck binding
sequence
but instead interacts with Grb2 (
37). PTP-PEST probably
corresponds to the p110 protein seen in testis, spleen, and thymus,
as
this protein, tyrosine phosphatase, is enriched in the immune
system. The other known Nck binding proteins, WIP, PRK2, NAP-4,
and
NAP-5, contain suitable target sequences (Fig.
5) but are
probably
lower-abundance proteins. Except in the case of PAK,
we have yet to
establish whether these proteins are in vivo Nck
targets; the
availability of Nck-deficient cells may help to resolve
this issue in
the
future.
The SH3[2] domain and Nck function in vivo.
The importance
of the SH3[2] domain is exemplified in Drosophila, where
photoreceptor cell projection to the optic ganglia requires the Nck
homologue Dock. In a dock-null background, expression of
Dock-containing mutations in SH3[1], SH3[3], or SH2 restores the
projection, but mutants of the SH3[2] domain do not (44). Myristoylated PAK can rescue the loss of Dock, indicating that PAK is a
key downstream component (19). This rescue requires the
function of both the p21-binding and kinase domains of PAK. Dock can
interact with the protein tyrosine phosphatase dPTP61F (10).
A putative Nck SH3[2] consensus binding sequence
PPPLPPRVQSLN335 is present in dPTP61F. Likewise, the
members of the mammalian PTP-PEST family contain similar Nck binding sequences.
The ability of membrane-targeted Nck to promote FC disassembly in
cultured mammalian cells through its SH3[2] PAK-binding
domain (data not shown) could be relevant to the function of Nck
in the
nervous system. R-cell projection patterns are abnormal
in
Drosophila Pak mutants, with axons forming unusually thick
bundles (
19). PC12 cells expressing kinase-inactive

PAK
exhibit
stunted neurite outgrowth patterns associated with an increase
in cellular FCs, whereas overexpression of wild-type

PAK leads
to
increased neurite outgrowth (
39). Growth factors that
stimulate
neurite outgrowth (which is a Cdc42- and Rac1-dependent
process)
probably thereby promote FC turnover through
PAK.
Regulation of PAK-SH3 interactions.
The affinity of the
well-studied Grb2 for SOS is decreased upon phosphorylation of four
sites within the proline-rich C-terminal end of SOS by
mitogen-activated protein kinases. This provides a means of controlling
Ras activation (11). Extracellular signals can also
stimulate specific dephosphorylation events that regulate SH3
interactions: a recent example involves
-arrestin recruitment by
G-coupled receptors, leading to dephosphorylation of the phospho-S412, thereby allowing interaction with the Src SH3 domain (29).
In the case of Nck, it seems likely that alternative partners are
recruited under different conditions. A prevalence of S
and T residues
C-terminal to the conserved arginine (PXXPXR) in
many Nck targets
suggests that these are negative regulatory sites.
The Nck-PAK-PIX
complex will remain stable at its site of action
(for example, FCs)
only as long as PAK remains in a basal or partially
active state (Fig.
8). It appears that activation of Nck-recruited
PAK occurs through both
Cdc42-dependent and -independent mechanisms
(
28) and
will be affected by local concentrations of GTP-Cdc42
or other factors.
Autophosphorylated PAK loses its affinity for
PIX, involving
phosphorylation of

PAK S198 and S203 (
30), which
flank
the C-terminal side of the PIX SH3 binding site as well
as Nck (or
perhaps related SH3s). Thus, wild-type kinase cycles
between cytosol
and PIX-containing FC sites, but when the catalytic
activity of PAK is
inhibited, it forms a stable association with
FCs (Fig.
9). The role of
Nck binding for FC localization is presently
not clear. PAK therefore
plays a role in RhoA-type FCs (because
it is continuously cycling
through these structures), although
at steady state we do not see it
concentrated at these sites.
Future studies looking at real-time FC
dynamics will be able to
address this issue. The down-regulation in
binding will generally
serve to limit PAK's disassembling action on
FCs. At present,
it is not clear why PAK is observed in Cdc42- and
Rac-induced
FCs, where the kinase is expected to be most active. Since
in
their active state these p21s themselves localize to FCs
(
30),
they might be responsible for shifting the PAK
distribution.
PAK dissociation also limits the effects of PIX, whose interaction with
its unique partner, PAK, is required for GEF activity
(
39)
and thus cytoskeletal effects, e.g., lamellipodium formation
(
32). Because formation of GTP-Rac1 itself leads to further
recruitment of PAK and associated PIX to the membrane, a mechanism
to
break this positive-feedback cycle is conferred by the loss
of PIX
binding upon PAK activation. In support of this, we and
others have
observed that kinase-dead PAK is more efficient in
driving
Rac-dependent lamellipodium formation through PIX (
39,
49)
as a consequence of the stabilization of the PIX-PAK complex.
That
these PAK effects might be independent of Rac1 (
50) seems
unlikely.
In conclusion, the SH3[2] domain of the adapter protein Nck is
capable of forming complexes with a number of target proteins
through a
preferred motif. The presence of a phosphorylatable
serine in the motif
may represent a general mechanism to regulate
binding. We observe that
other SH3 domains exhibit distinct subsets
of targets (Fig.
1),
probably based on different motifs flanking
the PXXP core, which may be
dissected using this peptide approach.
Among Nck binding proteins, the
phosphorylation states of target
sequences in vivo are clearly key
factors in regulating complex
formation. It will be of interest to see
if this mechanism is
widely
utilized.
 |
ACKNOWLEDGMENT |
This work is funded by the Glaxo Singapore Research Fund.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Glaxo-IMCB
Group, Institute of Molecular & Cell Biology, 30 Medical Dr., Singapore 117609, Singapore. Phone: (65) 874-6167. Fax: (65) 774-0742. E-mail: mcbmansr{at}imcb.nus.edu.sg.
 |
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Molecular and Cellular Biology, June 2000, p. 3906-3917, Vol. 20, No. 11
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