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Originally published In Press as doi:10.1074/jbc.M205282200 on July 1, 2002
J. Biol. Chem., Vol. 277, Issue 41, 38764-38771, October 11, 2002
Evidence for a Lectin Activity for Human Interleukin
3 and Modeling of Its Carbohydrate Recognition Domain*
Jean-Pierre
Zanetta §,
Roland
Bindeus ,
Guy
Normand¶,
Viviane
Durier ,
Philippe
Lagant ,
Emmanuel
Maes , and
Gérard
Vergoten
From the CNRS Unité Mixte de Recherche 8576, Glycobiologie Structurale et Fonctionnelle, Université des
Sciences et Technologies de Lille Bâtiment C9, 59655 Villeneuve
d'Ascq Cedex, France and the ¶ Physiologie Cellulaire et
Moléculaire de la Rétine, INSERM EPI9918, Hôpitaux
Universitaire de Strasbourg, 1 place de l'Hôpital, 67091 Strasbourg Cedex, France
Received for publication, May 29, 2002, and in revised form, June 27, 2002
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ABSTRACT |
We demonstrate that human interleukin 3 (IL-3) is
a lectin recognizing specifically the glycosaminoglycan part of a
chondroitin sulfate proteoglycan (PGS3; Normand, G., Kuchler,
S., Meyer, A., Vincendon, G., and Zanetta, J. P. (1988)
J. Neurochem. 51, 665-676) isolated from the
adult rat brain. The specificity of the interaction of this particular
proteoglycan with IL-3 is due to the abundance of
GlcA(2S) 1,3GalNAc(4S) 1 disaccharide units as suggested by 1H NMR. Computational docking experiments of the lower
energy conformers of the different disaccharides from chondroitin
sulfates reveal a privileged binding site for
GlcA(2S) 1,3GalNAc(4S) 1 (involving His-26, Arg-29, Asn-70, and
Trp-104) localized in an area of IL-3 different from the
receptor-binding domain previously identified by others (Bagley,
C. J., Phillips, J., Cambareri, B., Vadas, M. A., and Lopez,
A. F. (1996) J. Biol. Chem. 271, 31922-31928). Molecular modeling of the mutation P33G, described as increasing the biological activity of IL-3 without affecting its receptor binding
(Lokker, N. A., Movva, N. R., Strittmatter, U., Fagg, B., and
Zenke, G. (1991) J. Biol. Chem. 266, 10624-10631)
provokes a change of the three-dimensional structure of IL-3,
especially in the area of the putative carbohydrate recognition domain
defined above. Computational docking experiments of the different
disaccharides of chondroitin sulfates indicate a loss of
affinity for the previous ligand but a higher affinity for
the classic disaccharide of chondroitin-4-sulfate. This change
from a rare and specific ligand to a more abundant constituent of
proteoglycans could induce an increased quantitative association
between the IL-3 receptors and its ligands and, consequently, an
increased signaling.
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INTRODUCTION |
Interleukin 3 (IL-3) is a member of the cytokine superfamily that
promotes multipotential hematopoietic cell growth by interacting with a
cell surface receptor composed of - and -chains and possessing a
domain necessary for signaling but not for receptor binding. We
made the hypothesis that this domain could be a carbohydrate recognition domain (CRD)1 as
evidenced for several interleukins (1, 2) able to specifically associate the interleukin receptor with other surface complexes expressing the carbohydrate ligand of the interleukin. In previous experiments (1),2 none of the
tested cytokines was able to bind significantly to mixtures of
commercially available glycosaminoglycans (GAG). These negative
results were surprising because several studies (3-5) reported
interactions of cytokines with proteoglycans. The negative results of
our previous studies could, at least in part, be explained by the use
of a different methodology. In fact, our method (1) measured by
immunoblotting the quantity of unlabelled recombinant human cytokine
unbound to plastic microwells containing or not containing immobilized
putative ligands. Consequently, binding could be observed only when the
ligand was present at a stoichiometric level with the cytokine and when
the affinity of the cytokine for its ligand was sufficiently high.
Because GAGs present large structural varieties and because the
commercial GAGs used in the previous study (1) were isolated from
non-mammalian organisms, we decided to test the binding of different
cytokines to different immobilized proteoglycans previously isolated
from the adult rat brain (6).
This study demonstrates the specific binding of IL-3 to a chondroitin
sulfate proteoglycan isolated from adult rat brain. This
compound possesses an unusually high degree of sulfation, with the
majority of the disaccharide units formed of 2-O-sulfated glucuronic acid and of 4-O-sulfated
N-acetylgalactosamine as suggested by 1H NMR of
its glycosaminoglycan part. Computational docking of the lower energy
conformers of the disaccharides from chondroitin-4-sulfate and
chondroitin-6-sulfate, chondroitin-4,6-disulfate,
chondroitin-2,4-disulfate, and chondroitin-2,6-disulfate results in a
specific docking of GlcA(2S) 1,3GalNAc(4S) 1 in the area of
Trp-104 previously proposed as a domain of IL-3 necessary for
its function. Molecular modeling of the mutation P33G that gives a
mutein with increased biological activity (7, 8) indicates a complete
modification of this domain (with the complete accessibility of
Trp-104). In silico docking of all disaccharides
described above indicates that the theoretical best ligand is
no more GlcA(2S) 1,3GalNAc(4S) 1 but the classic disaccharide
derived from chondroitin-4-sulfate. These data suggest that the
increased activity of the P33G mutein is due to a change from a rare
disaccharide ligand to a common disaccharide ligand, allowing the
increase of IL-3-dependent signaling.
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MATERIALS AND METHODS |
Chemicals--
Interleukin 1 (IL-1 ), -1 , -3, -5, -7 and
-8, interferon- (IFN ), and their respective polyclonal antibodies
were purchased from Chemicon (Temucula, CA). Monoclonal anti-rabbit
IgG, chondroitin sulfate A, B, and C, heparan sulfate, heparin,
hyaluronic acid, keratan sulfate, bovine serum albumin, nitro blue
tetrazolium (NBT), 5-bromo-4-chloro-3-indolyl-phosphate (BCIP), and
cetyl-pyridinium chloride (CPC) were from Sigma. Nitrocellulose (0.45 µm pore size) was from Schleicher & Schuell (Darmstadt, Germany).
D2O (99.97% purity; Euriso-top®) was from CEA
(Saclay, France). Periodate-treated bovine serum albumin was prepared
according to Glass et al. (9).
Isolation of Rat Brain Proteoglycans--
In typical
preparations, 240 forebrains (from adult Wistar albino rats) were
homogenized (5% w/v) in 10 mM Tris-HCl buffer, pH 7.2, containing protease inhibitors (10 mM EDTA, 100 mM 6-amino-hexanoate, and 5 mM benzamidine
hydrochloride) and centrifuged for 2 h at 100,000 × g. The supernatant and the particulate fractions were treated separately.
The particulate fraction (M fraction) was delipidized (10) and
extracted by stirring for 24 h at 4 °C in 0.1 M
sodium citrate buffer, pH 3.1, containing the protease inhibitors as
above. After centrifugation for 1 h at 23,000 × g, the supernatant was discarded, and the pellet was
extracted for 48 h at 4 °C in 50 mM Tris-HCl buffer, pH 7.5, containing 4 M guanidinium chloride and
protease inhibitors as above. After centrifugation (1 h at 15,000 × g), the pellet was discarded, and the supernatant was
dialyzed against large volumes of cold water. The precipitate was
recovered by centrifugation (1 h at 23,000 × g) and
extracted again in 0.4 M sodium citrate buffer, pH 5.0, over 24 h at 4 °C. After centrifugation, the supernatants were
passed on a DE-52 column (17 × 2.5 cm) previously equilibrated in
0.1 M sodium citrate buffer, pH 5.0. Proteoglycans were
eluted with a linear gradient of NaCl from 0 to 1.0 M with a total volume of 200 ml at a flow rate of 30 ml/min. The fractions containing proteoglycans were dialyzed against cold water and lyophilized. After solubilization in a small volume of water, the
proteoglycans were precipitated with ethanol (11). The pellet was
homogenized in 4 ml of 10 mM Tris-HCl buffer containing 0.4 M NaCl and centrifuged (30 min at 10,000 × g) at room temperature. The supernatant was submitted to gel filtration.
The supernatant fraction of the first extract (S fraction) was
precipitated with 0.1% CPC for 24 h at 4 °C (12), and the supernatant was discarded. The pellet was extracted in 50 mM Tris-HCl, pH 7.5, containing 4 M guanidinium
chloride and protease inhibitors. Subsequent procedures were
identical to those for the M fraction.
The material enriched in proteoglycans was fractionated by gel
filtration on an Ultrogel AcA22 column (100 × 2.5 cm) previously equilibrated in 10 mM Tris-HCl buffer, pH 7.5, containing
0.4 M NaCl. The elution was followed by measuring the
absorbance at 280 nm and using the carbazole technique (13). Seven
different proteoglycans were isolated, four from the M fraction (PGM1,
PGM2, PGM3, and PGM4) and three from the S fraction (PGS1, PGS2, and PGS3). The nature of these compounds was tested using enzymatic degradation (chondroitinase AC and ABC), nitrous acid treatment (6),
and gas chromatography/mass spectrometry (GC/MS) of heptafluorobutyrate derivatives of the mono- and disaccharides liberated after
acid-catalyzed methanolysis in the presence of barium acetate (14).
For preliminary experiments of binding of cytokines, another
preparation of proteoglycans was used, consisting of the material obtained applying the previous procedure without initial separation of
the M and S fractions and without separation by gel filtration.
Immobilization of Proteoglycans on Plastic
Microwells--
Mixtures of proteoglycans or individual compounds were
dissolved or suspended in excess (1 mg/ml) in PBS (25 mM
sodium phosphate buffer, pH 7.2, containing 150 mM NaCl)
and 50 µl were added to each microwell. The liquid was evaporated at
50 °C in an oven. The wells were rinsed three times with PBS and
then saturated three times for 2 h at room temperature with 300 µl of a 3% solution in PBS of bovine serum albumin previously
treated with periodate (9). This treatment eliminated interferences due
to the presence of glycoconjugates in commercially available bovine
serum albumin preparations. The wells were rinsed three times with PBS
and then water. Before use, the wells were saturated again as above and rinsed three times with PBS. Cytokines were added (100 ng in 50 µl of
PBS containing 0.3% periodate-treated bovine serum albumin) and left
for 2 h at room temperature under rotary agitation. The supernatants were recovered, supplemented with 25 µl of Laemmli (15)
dissociating buffer, boiled for 10 min, and submitted to 13%
acrylamide SDS-PAGE in the Laemmli buffer system. The gels were blotted
onto nitrocellulose (16). The cytokines were revealed using their
respective polyclonal anti-cytokine antibodies, followed by alkaline
phosphatase (AKP)-labeled anti-rabbit IgG, and finally NBT/BCIP
detection of the AKP activity (17).
Purification of the PGS3-derived Glycosaminoglycan--
Purified
PGS3 was submitted to mild alkaline hydrolysis (0.1 M NaOH
overnight at 4 °C with stirring) in order to liberate O-linked glycans (GAGs and eventually O-glycans).
The sample was neutralized with 0.5 M HCl and then dialyzed
(24 h at 4 °C) against precooled distilled water. The dialysate and
the remaining samples were dried under vacuum at room temperature in a
rotary evaporator. The material retained in the dialysis tube (likely
containing GAGs and proteins) was centrifuged, and the supernatant was
precipitated with 0.1% CPC overnight at 4 °C. After centrifugation,
the pellet was suspended in water, and excess CPC was extracted three
times with isoamyl alcohol. The remaining aqueous phase was evaporated to dryness, and the sample was exchanged against D2O for
1H NMR analysis.
NMR Analysis of the PGS3 Glycosaminoglycan--
Prior to NMR
spectroscopic analysis, the sample was repeatedly exchanged in
D2O with intermediate freeze-drying and then dissolved in
250 µl of D2O. The sample was analyzed in 200 × 5 mM BMS-005-B Shigemi® tubes at 300 and 315 K
on a Bruker ASX400-NB spectrometer (1H 400.33MHz,
Centre Commun de Mesure RMN, Villeneuve d'Ascq, France) equipped with
a double resonance (1H/X) broadband inverse z-gradient
probe head. Data were recorded without sample spinning, and chemical
shifts were expressed in ppm downfield from the acetone proton signal
( 1H, 2.225 ppm).
Molecular Modeling of the Disaccharide Ligands of IL-3--
The
structures of low energy conformers of the disaccharide ligand of IL-3
were obtained using the minimization and random searching tools within
the SYBYL 2002 version (SYBYL, Tripos Inc., St Louis, MO;
www.tripos.com). Parameters for the internal rotation potentials are
those obtained in our group.3
The electrostatic charges were derived from quantum mechanical calculations using the Jaguar software (Jaguar version 4.0, Schrödinger Inc., Portland, OR; www.schrodinger.com). The density
functional theory was used at the B3LYP/6-31G* level. For that
purpose, the molecular electrostatic potential has been fitted to a set
of point charges located at the atomic centers, reproducing the dipole moment. The electrostatic potential itself was computed on a spherical grid. A random conformational search technique was used to sample the
conformational space. The two glycosidic linkage rotatable bonds
and five rotatable bonds for substituents were defined. The
structures of low energy conformers were then compared with those of
disaccharides of classic chondroitin sulfate. In all cases, 20,000,000 configurations were examined using bump checking (with a van der Waals
scaling factor of 0.7) and energy as criteria.
In Silico Docking of the Chondroitin Sulfate Disaccharides in the
IL-3 Molecule--
For the five lower energy conformers of the five
disaccharides of chondroitin sulfates, a surface docking with IL-3 (PDB
1JL1) has been investigated. The Global Range
Molecular Matching (GRAMM, 2002 version)
program was used (18). This technique locates the area of the global
minimum of intermolecular energy for the structure, with different
accuracy. The generic mode and a grid step of 1.7 were used. 1000 matches were stored, among which 100, 10, and 5 were displayed. For the
lower energy disaccharide/IL-3 complexes, a dynamic energy-based
optimization was performed. The data of the conformations of the
disaccharides and of the docking experiments were analyzed as PDB files
using the Swiss-Pdb-Viewer (www.expasy.ch) and/or the Weblab ViewerLite
4.0 and 4.2 (www.msi.com). For the computational study of the
possible modification of the three-dimensional structure of IL-3 under
the effect of specific mutations, amino acids were altered using the
mutate option of the SYBYL software, followed by the classic program of
energy minimization for the whole molecule.
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RESULTS |
Using the technique described above (see "Materials and
Methods"), none of the cytokines bound to a mixture of commercially available glycosaminoglycans (not shown; see Ref. 1 for IL-1 , -1 ,
-4, -6, and -7). Because binding of cytokines to proteoglycans was
reported, we tested the binding of these cytokines to a mixture of
proteoglycans isolated from the adult rat brain (6). As shown in Fig.
1A, the different cytokines
showed different behavior. IL-1 , -5, and -7 did not show any
binding. The same was found for IL-1 and interferon- despite the
low efficiency of the antibodies used here. The behavior of IL-8 could
not be studied; the antibody always gave negative results even when
IL-8 was directly submitted to SDS-PAGE and blotting, probably because
of the specific antibody reactivity against the non-denatured form of
IL-8. In contrast, IL-3 showed an important binding to this mixture,
which was considered as specific because it was not observed in wells
lacking the proteoglycans (Fig. 1A) and was the only
cytokine showing a strong binding.

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Fig. 1.
Immunoblotting study of the fixation of
different cytokines to the mixture of rat brain proteoglycans
(A), the fixation of IL-3 to the different isolated
rat brain proteoglycans (B), and inhibition of the
fixation to PGS3 (C). In A,
B, and C, + corresponds to wells containing
immobilized proteoglycans and to wells not containing
proteoglycans. A, note the complete fixation of 100 ng IL-3
to the proteoglycan mixture. B, note the complete fixation
of IL-3, to 1 µg of immobilized PGS3, and the total absence of IL-3,
to 10 µg of immobilized PGM1, PGM3, PGS1, and PGS2. IL-3 showed a
partial binding to 10 µg of immobilized PGM2. C, binding
to PGS3 (lane T, +) was not inhibited by the
dialyzable oligosaccharides (lane 1, +) but with
10 µg of the purified GAG portion of PGS3 (lane
2, +). The quantity of IL-3 was equivalent to that recovered
in wells uncoated with PGS3 (lane T, ).
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The different behavior of IL-3 on mixtures of GAGs and on mixtures of
different proteoglycans was surprising, because the proteoglycan
mixture actually contained chondroitin sulfate A and B, keratan
sulfate, heparan sulfate, and hyaluronic acid (the latter found as a
contaminant in the preparations). Because this mixture contained seven
different proteoglycans (6), four derived from the membrane fraction
(PGM1, PGM2, PGM3, and PGM4) and three from the soluble fraction (PGS1,
PGS2, and PGS3) of adult rat brain, these components were individually
immobilized on plastic microwells. When the wells were supplemented
with 100 ng of IL-3, 20 and 90% of IL-3 were bound to PGM2 and PGS3,
respectively (Fig. 1B). The binding to PGM1, PGM3, PGM4,
PGS1, and PGS2 was negligible in contrast with PGS3 (90 ng for 1 µg
of immobilized PGS3, instead of 20 ng for 10 µg of immobilized PGM2).
Enzymatic and chemical degradations (6) and GC/MS analysis (14)
allowed precise measurement of the specificity of the binding of IL-3.
Indeed, PGM1 was a mixture of hyaluronic acid and a proteoglycan
containing heparan sulfate and a chondroitin sulfate chain, whereas
PGM2, PGM3, and PGM4 were similar but were not contaminated with
hyaluronic acid. In contrast, PGS1, PGS2, and PGS3 were all chondroitin
sulfate proteoglycans devoid of heparan sulfates and dermatan sulfate,
as verified by the complete degradation of the GAG portion using
chondroitinase AC (6). Therefore, it was suggested that the ligand of
IL-3 was a chondroitin sulfate proteoglycan. The absence of
characteristic disaccharides released from heparan sulfates and the
absence of iduronic acid, together with the unique presence of
disaccharides derived from chondroitin sulfates, observed by GC/MS (14)
verified these conclusions.
Based on chemical analysis (6), PGS3 differed from the other
proteoglycans by its higher ratio of sulfate relative to GalNAc (1.63/1.00), between 0.34 for PGM3 and 0.81 for PGS2. Throughout the
different proteoglycans of the M fraction, PGM2 also showed a higher
degree of sulfation. This higher level of sulfation might explain the
specific binding of IL-3 to these particular chondroitin sulfate brain
proteoglycans and not to the others, as well as to commercially
available A and C chondroitin sulfates.
Inhibition of IL-3 Binding to PGS3 by the GAG Portion of
PGS3--
To determine the nature of the interaction between PGS3 and
IL-3, we performed inhibition experiments of the binding with glycans
isolated from PGS3. In fact, the monosaccharide analysis of PGS3 (6)
revealed the presence of a significant amount of mannose in the
molecule, indicating the presence of O- or
N-linked glycans. Consequently, it was necessary to confirm
that the binding of IL-3 to PGS3 was not because of these glycans.
Therefore, after a mild -elimination procedure, the small
oligosaccharides were dialyzed and separated from the non-dialyzable
material, including chondroitin sulfate chains and the protein portion
(possibly associated with N-glycans). The two different
fractions were tested for their inhibitory properties for the binding
of IL-3 to the immobilized intact PGS3. As shown in Fig. 1C,
the dialyzed material was not inhibitory, in contrast with the
non-dialyzable material (not shown). The inhibitory material was
purified by precipitation with CPC. As shown in Fig. 1C,
only the GAG portion of PGS3 was inhibitory. Therefore, these
experiments demonstrated that the high affinity ligand of IL-3 was the
GAG portion of PGS3. The specificity of the binding of IL-3 to PGS3 was
likely due to its peculiar sulfation pattern, because chondroitin 4 and
6 sulfates from whale cartilage (Sigma) were inactive.
Determination of the Position of the Sulfate Groups of
PGS3--
To determine the positions of the sulfate groups in the
chondroitin chain, the glycosaminoglycan part of PGS3 liberated by mild
alkaline hydrolysis (see "Materials and Methods") was submitted to
1H NMR analysis at 300 and 315 K. The chemical shifts of
different protons indicated that, despite an heterogeneity, the
majority of the material was composed of GlcA sulfated in position 2 and of GalNAc sulfated in position 4. Indeed, no signal was detected for the H2 protons of GlcA at 3.375-3.379 ppm (19-22)
characteristic of non-sulfated GlcA and around 3.64 ppm characteristic
of 3-sulfated GlcA. In contrast, the characteristic downfield-shifted
signal at 4.11 ppm of 2-sulfated GlcA (20) was observed. This
conclusion was reinforced by the presence of the downfield-shifted
signal (4.80 instead of 4.45 ppm) of the anomeric proton of GlcA. This indicated that at least 90% of the GlcA residues were sulfated in
position 2. For GalNAc, two signals corresponding to the H4 protons
were detected at 4.19 and 4.75 ppm in the proportion 1:2, indicating
the presence of both non-sulfated GalNAc at 4.19 ppm and 4-sulfated
GalNAc at 4.75 ppm (22). Therefore, these data indicated that the major
disaccharide repetitive units of PGS3 were
GlcA(2S) 1,3GalNAc(4S) 1-, the other being
GlcA(2S) 1,3GalNAc 1- (in a molar ratio of 2:1).
Molecular Modeling of the Disaccharide Ligands of
IL-3--
The conformations of the lower energy conformers of the
disaccharide ligand of IL-3 GlcA(2S) 1,3GalNAc(4S) 1 were
calculated and compared with the conformations of the disaccharides of
classic chondroitin sulfate A, GlcA 1,3GalNAc(4S) 1, and
chondroitin sulfate C, GlcA 1,3GalNAc(6S) 1, and with those of
GlcA(2S) 1,3GalNAc(6S) 1 and of GlcA 1,3GalNAc(4,6S) 1. As
shown in Fig. 2, the five lower energy
conformers of the disaccharide ligands of IL-3,
GlcA(2S) 1,3GalNAc(4S) 1, showed two groups of compounds, with the
different energy in each group caused by the presence of different
intramolecular hydrogen bonds. Compound A in Fig. 2 showed
the lowest energy (0.7 kcal·mol 1 lower than compound
B and 1.2 kcal·mol 1 lower than the three
other conformers). These five lower energy conformers differed from the
others by a jump in energy of higher than 5 kcal·mol 1.

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Fig. 2.
Calculated conformations of the five lower
energy conformers of the
GlcA(2S) 1,3GalNAc(4S) 1
disaccharide. Compound A is the lower energy
conformer. Compounds B, C, D, and
E showed increased energies of 0.76, 1.233, 1.395, and 2.105 kcal·mol 1 relative to compound A.
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In Silico Docking of the Ligands of IL-3 in the IL-3
Molecule--
For the five families of disaccharides, the five lower
energy conformers were submitted to computational docking into the three-dimensional structure of IL-3, accessible as PDB 1JL1. The
non-ligand oligosaccharides showed a quasi-random distribution with a
predominance of localization in the area containing His-95 and -98 (not
shown), with fine analysis showing that the major interactions were of
ionic nature. Because the calculations were performed in
vacuo ( = 1), these types of interactions were considered very unlikely to take place in vivo. The absence of van der
Waals interactions and/or hydrogen bonds with the surrounding amino acids reinforced this conclusion. This was not the case for the lower
energy conformers of GlcA(2S) 1,3GalNAc(4S) 1 because 70% of them
were found in the area of His-26, Arg-29, Asn-70, and Trp-104 (Fig.
3A). When the experiments
included only the 10 energy conformers of the IL-3 ligand, the
partition became 3 to 7 in the same sites (Fig. 3B). This
ratio was 1:4 for the five lower energy conformers of the ligand of
IL-3 (Fig. 3C).

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Fig. 3.
Views of the computational docking of the 100 (A), 10 (B), and 5 (C) lower energy complexes of the lower energy
conformer (Fig. 2, compound A) of
GlcA(2S) 1,3GalNAc(4S) 1
into the three-dimensional structure of human IL-3 (PDB
1JL1).
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The fine analysis of the results of the docking experiments of the five
lower energy conformers indicated a preferential localization of four
of them in close apposition to the Trp-104 residue. The exception was
one that localized in the area of His-95 and -98 (Fig. 3C).
As discussed above, this site was rejected as a putative CRD because of
the predominance of ionic bonds and the absence of van der Waals
interactions. The other conformers all localized in the same region,
and all interacted with Trp-104 through strong van der Waals
interactions and hydrogen bonding with surrounding amino acids. As
shown in Fig. 4A, for the
lower energy conformers (shown in Fig. 2) this site was essentially
different from that defined (23) as the receptor-binding site of IL-3
(Fig. 4A, blue). The fine analysis of the docking
data of the four lower energy conformers of
GlcA(2S) 1,3GalNAc(4S) 1 indicated the same major features, van der
Waals interactions with Trp-104 and His-26 and hydrogen bonds with the
same amino acids. After energy minimization of the complexes, the lower
energy was found for a disaccharide ligand presenting an intermediate
conformation between conformers A and B of Fig. 2
without modification of the conformation of the protein.

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Fig. 4.
A, representation of the putative
carbohydrate recognition domain of human interleukin 3. Trp-104 is
shown in yellow, the disaccharide ligands
GlcA(2S) 1,3GalNAc(4S) 1 in green, and amino acids
involved in the formation of hydrogen bonds with the ligands in
purple. The amino acids proposed as part of the
receptor-binding domain (23) are shown in blue. The Pro-33
residue mutated to Gly in B is in red.
B, calculated conformation of the P33G mutein and
computational docking of GlcA 1,3GalNAc(4S) 1- into the mutein.
Note that the area of the putative CRD of wild-type IL-3 is completely
modified, whereas modifications were less evident in the
receptor-binding domain.
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The precise interactions of this compound with the structure of
IL-3 (Fig. 5A) showed a very
intense van der Waals interaction of the pyranic ring of GalNAc facing
the indolic group of Trp-104 (2.86-4.16 Å). Four hydrogen bonds
stabilized the binding. There was one hydrogen bond (2.68 Å) between
the oxygen of the sulfate group of GlcA and the nitrogen atom of
the lateral chain of Asn-70, one hydrogen bond (2.61 Å)
between the oxygen atom of the sulfate group of GalNAc and the nitrogen
atom of the side chain of Asn-70, one hydrogen bond (2.78 Å) between
the oxygen of the polypeptide amide bond of His-26 and the oxygen atom
of the carboxylic group of GlcA, and one hydrogen bond (2.94 Å)
between the nitrogen atom of the guanidinium group of Arg-29 and the
oxygen atom of the carboxylic group of GlcA. A weaker van der Waals
interaction was also observed between the pyranic ring of GlcA and the
side chain of His-26 (4.79-6.59 Å). This configuration (with two
series of van der Waals interactions and four strong hydrogen bonds)
fulfilled the common criteria defined for the binding of
disaccharides in the CRD of calcium-independent lectins (24-26).
Furthermore, this site was clearly different from the receptor-binding
domain as defined by site-directed mutagenesis experiments. Finally,
the importance of Trp-104 for the activity of IL-3, but not for its interaction with the receptor, was also clearly identified (27). Therefore, it was suggested that the site defined above actually contained the carbohydrate recognition domain of human IL-3, identified by its strong interaction with the PGS3 proteoglycan.

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Fig. 5.
Magnification of the results of docking
experiments of the high affinity ligand of IL-3 into the putative
carbohydrate recognition domain of IL-3 (A) and
computational effect of the mutation R29Q (B).
A, the formation of four hydrogen bonds between the IL-3
ligand and Asn-70, His-26 (back), and Arg-29 in the
crystallized IL-3. Note that the hydrogen bond of the ligand with
Arg-29 in A finds its equivalent with Gln-29 in
B, the latter corresponding to the wild-type human IL-3.
C, view of the putative CRD of IL-3 showing the van der
Waals interactions between the pyranic rings and Trp-104 and His-26
(hydrogen atoms were stripped in order to render the picture clearer).
D, proposed binding site of the classic disaccharide of
chondroitin-4-sulfate in the P33G mutein.
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In Silico Determination of the Three-dimensional Structure of the
P33G IL-3 Mutein--
It was previously shown (7, 8) that the P33G
mutation provoked 14-fold increased biological activity for the mutein relative to the wild-type recombinant human IL-3. Although the previous
authors (7, 8) did not demonstrate strong modification of the
three-dimensional structure after the mutation, our in silico studies indicated that the conformation of the mutein (Fig. 4B) was significantly different from that of the non-mutated
protein (Fig. 4A). Although the site defined by Bagley
et al. (23) as the receptor-binding domain was relatively
preserved, the P33G mutation rendered a complete accessibility of
Trp-104 and an opening of the cavity in which the IL-3 ligands were
initially computationally localized. Especially, the amino acids
(His-26, Arg-29, Gln-70) involved in the formation of strong hydrogen
bonds with the IL-3 ligand showed a completely modified localization.
Therefore, we performed in silico docking
experiments of the five lower energy conformers of the initial IL-3
ligands into the mutein and, for comparison, of the four other
disaccharide constituents of chondroitin sulfates mentioned above. In
all cases, more than 50% of the lower energy conformers of all
disaccharides were localized in the giant cavity of the mutein.
However, fine analysis of the interaction of the lower energy
conformers of GlcA(2S) 1,3GalNAc(4S) 1- with the calculated
structure of the P33G mutein showed insufficient van der Waals
interactions and hydrogen bonding for consideration of this area as a
putative CRD for this compound. All the lower energy conformers of
GlcA(2S) 1,3GalNAc(4S) 1 present in this cavity showed very weak
van der Waals interactions with Trp-104 (more than 10 Å) and a maximum
of one hydrogen bond with surrounding amino acids. When performing the
fine analysis of the results of the docking experiments mentioned
above, only the classic disaccharide from chondroitin-4-sulfate
(GlcA 1,3GalNAc(4S) 1-) showed 50% of the lower energy
disaccharide/mutein complexes localized close to Trp-104 (Fig.
6). Some of these complexes showed
interesting features, such as relatively high van der Waals
interactions between the pyranic ring of the 4-sulfated GalNAc and
Trp-104 and two hydrogen bonds between the oxygen atom of the sulfate
group and the carboxyl group of Asp-103 (Figs. 4B and
5D). Furthermore, additional van der Waals interactions
could be possible with Pro-31 and Phe-107, with the three cyclic amino
acids constituting a cradle for the disaccharide of
chondroitin-4-sulfate. Consequently, these data suggested that in the
P33G mutein the putative calculated CRD specific for
GlcA(2S) 1,3GalNAc(4S) 1 changed to a site unable to recognize the
previous ligand of IL-3. In contrast, it was suggested that it could
recognize, but with a lower affinity, the classic disaccharides of
chondroitin-4-sulfate, GlcA 1,3GalNAc(4S) 1.

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|
Fig. 6.
Hypothetical schematic drawing explaining the
increased activity of the P33G mutein of IL-3. A, the
wild-type IL-3 (black) bound to IL-3R associates the
latter to a signal-transducing complex associated with a chondroitin
sulfate proteoglycan (purple) containing the rare
GlcA(2S) 1,3GalNAc(4S) 1- disaccharide units, thus generating a
signal (s). The majority of the signal-transducing complexes
associated with the same chondroitin sulfate containing the abundant
GlcA 1,3GalNAc(4S) 1- disaccharide units are not able to generate a
signal. B, the situation is completely reversed, and the
mutein (mIL-3, red) associates IL-3R to
several signal-transducing complexes, generating increased signaling
and, consequently, an increased biological response.
|
|
 |
DISCUSSION |
Specificity of IL-3 for the GlcA(2S) 1,3GalNAc(4S) 1
Disaccharide--
Several studies have reported the interactions of
cytokines with glycosaminoglycans (3-5). However, using a new
procedure involving unlabeled cytokines (1), we were unable to
demonstrate such specific interactions with commercially available GAGs
because this method (analysis of the quantity of unbound cytokines to immobilized ligand by immunoblotting) was only able to reveal stoichiometric interactions with the immobilized ligand. Furthermore, a
significant binding could be detected safely only if at least 10% of
the added cytokine were bound. Such a situation never occurred for five
cytokines (1) and for seven other cytokines (this study),4 although bindings to
commercially available GAGs were detected using labeled cytokines or
ELISA techniques (28-31). To analyze these different behaviors, we
decided to study the binding of cytokines to proteoglycans isolated
from the rat brain (6). This demonstrated that IL-3 recognized,
specifically, throughout the different proteoglycans isolated from
adult rat brain, the chondroitin sulfate proteoglycan PGS3. This
low Mr proteoglycan (Mr
100,000 obtained by gel filtration; Ref. 6) differed from the others by
its higher degree of sulfation. Although the oligosaccharide composition of PGS3 was complex (especially in the presence of a
significant amount of mannose), the binding of IL-3 to this compound
was directed to its GAG portion. In fact, all the mannose of PGS3 was
recovered in the dialyzable fraction after -elimination, indicating
that it was O-linked. Such oligosaccharides were frequently identified in brain proteoglycans (32-36). However, the
dialyzable fraction containing these compounds did not show a strong
ability for inhibition of the binding of IL-3 to PGS3. In contrast, the interaction was stoichiometrically inhibited by the GAG portion isolated from PGS3.
The higher degree of sulfation was likely necessary for the binding of
IL-3 because the majority of the other brain chondroitin-sulfate proteoglycans and commercially available glycosaminoglycans did not
show any affinity for IL-3. 1H NMR studies indicated that
the particularity of PGS3 consisted in the abundance (2:3) of the
disaccharide units GlcA(2S) 1,3GalNAc(4S) 1, a relatively rare
disaccharide previously identified in dog mastocytoma (37).
Definition of the Putative CRD of IL-3--
The computational
docking experiments of the lower energy conformers of five different
disaccharides derived from chondroitin sulfates in the
three-dimensional structure of IL-3 (38, 39) sustained the data
obtained by our binding and 1H NMR studies of the GAG
portion of PGS3. Indeed, intimate binding was only obtained for
GlcA(2S) 1,3GalNAc(4S) 1 and not for the other compounds. However,
it should be stressed that the three-dimensional structure of IL-3
accessible in the literature was not that of the wild-type human IL-3
but a mutated protein (38, 39), in contrast to the IL-3 used here in
binding experiments. In fact, the recombinant protein used for the
three-dimensional structure determination (38, 39) lacked the 1-13
N-terminal amino acids and the C-terminal residues (126-133). These
deletions of the N- and C-terminal portions of IL-3 did not introduce
modifications of the receptor binding nor of biological activity on
cell cultures. Furthermore, several mutations were performed (V14A,
N18I, T25H, Q29R, L32N, F37P, G42S, Q45M, N51R, R55T, E59L, N62V, S67H,
and Q69E). Nevertheless, this mutated protein was shown to be identical to the wild-type IL-3, both for its receptor binding and its biological activity on the same cells (38). Therefore, it was suggested that the
three-dimensional structure used for the docking experiments was very
close to that of the wild-type IL-3 used by us in binding experiments.
At least, essential structural features necessary for the full
expression of the biological activity of IL-3 and for its receptor
binding were preserved. In fact, all these mutations relative to the
wild-type were mutations of surface amino acids not involved in the
stabilization of the three-dimensional structure of IL-3. Except
for the Q29R mutation, all were concerned with the receptor-binding
domain and with the putative CRD of IL-3 calculated here. The reason
why the Q29R mutation did not provoke modifications of the biological
activity of IL-3 was explained by computational calculation of the
docking of GlcA(2S) 1,3GalNAc(4S) 1- in the Q29R mutein. As shown
in Fig. 6B, these calculations indicated that the more
stable conformation of the complex between the ligand and IL-3 involved
the same pattern of van der Waals interactions and hydrogen bonds. The
hydrogen bond between the oxygen atom of the carboxylic group of GlcA
and the nitrogen atom of the amide group of the lateral chain of Gln-29
was equivalent to that between the same carboxyl group and the nitrogen
atom of the guanidinium group of Arg-29. Therefore, it was suggested
that the three-dimensional structure of IL-3 reported in the literature
constituted a correct model structure for our docking experiments.
The site defined here as a putative CRD was essentially
different from those proposed as the receptor-binding domains. Indeed, site-directed mutagenesis (7, 8, 23, 27, 40-43) of human IL-3 defined
essential amino acids for binding to the IL-6R and -3R as
residues Ser-17, Asn-18, Asp-21, Arg-22, Thr-25, Ser-42, Glu-43,
Gln-45, Asp-46, Met-49, Arg-94, Pro-96, Arg-108, Lys-110, Leu-111,
Phe-113, Lys-116, and Glu-119. Deletion of the first 14 amino acids
(40) did not modify the receptor binding of IL-3, a property lost when
the first 18 amino acids were deleted (8). No biological activity was
found after deletion of the 22 C-terminal amino acids (8). Other
mutations (27) defined another site involving residues Trp-104,
Asn-105, Lys-110, and Arg-108 as necessary for the activity but not for
receptor binding.
Unfortunately, extensive mutagenesis studies were not performed in the
site that we propose as the CRD of IL-3 with the exception of Trp-104,
which suppressed the activity of IL-3, and the mutation Q29R, which did
not change the biological activity of IL-3. This was in agreement with
our own computational data on the interaction of the high affinity
ligands of IL-3 with these residues. Therefore, our biochemical and
docking experiments propose that the second site of IL-3, not necessary
for the binding to the IL-3R but for the biological activity of
IL-3, corresponds to its carbohydrate recognition domain. It involves a
strong van der Waals interaction between the pyranic ring of GalNAc and
Trp-104, a weak van der Waals interaction with His-26, and four strong
hydrogen bonds with His-26, (Arg/Gln)-29, and Asn-70. The configuration
of this site fulfilled the common features observed for the CRDs of
calcium-independent lectins (24-26). This putative CRD of IL-3 is also
very similar to that calculated for the CRD of IL-6 in interaction with
its HNK-1 type oligosaccharide ligand (2).
Calculated Changes of the Carbohydrate Specificity of the P33G
Mutein--
Mutations close to the putative carbohydrate recognition
domain defined above (P33N and P33G) increased the biological activity of IL-3 without significant effect on IL-3R binding (7, 39). Especially, the P33G mutation increased the activity of IL-3 by a
factor of 14 without significant changes of the binding to IL-3R (8). Based on the computer software now available, the authors concluded that this mutation did not provoke essential modifications of
the three-dimensional structure of IL-3. Using the Sybyl software, it
was evident that the structure of IL-3 was fundamentally changed, with
an opening of the molecule and the complete solvent accessibility of
the Trp-104 residue. This initially suggested to us a stronger interaction between IL-3 and its ligand, a property that could explain
the increased biological activity of the P33G mutein. In fact, the
docking experiments contradicted this view, because they indicated that
the ligand of IL-3 did not find a significant binding in the region of
the putative CRD determined above. In contrast, some lower energy
conformers of the disaccharide derived from chondroitin-4-sulfate
showed rather good interactions with Trp-104 and the surrounding amino
acids. Therefore, it was suggested that the increased biological
activity of the P33G mutein could be related to a change in the nature
of its chondroitin sulfate ligand.
Indeed, as determined previously for IL-2 (44) and for IL-6 (2),
the function of the CRD of the cytokine is the association of its
receptor complexes with another surface molecular complex containing
the oligosaccharide ligands. This specific extracellular association,
due to the bifunctional cytokine, induces specific phosphorylation/dephosphorylation mechanisms (45). A change in
specificity of oligosaccharide ligands could induce a change in
biological activity without modification of the binding to the
receptor. In the case of IL-3, the change from a rare
chondroitin sulfate structure (for the wild-type IL-3) to an abundant
structure (for the P33G) mutein could produce an increased number of
interactions and, consequently, a more intense signaling (Fig. 6). It
is worth mentioning that eosinophils and mast cells (or derived cell
lines), which are extremely sensitive to IL-3 and were used for testing the effect of mutations on the biological activity of IL-3, contain a
significant proportion (6-16%) of disulfated disaccharides (46-48), the remainder being essentially constituted of
chondroitin-4-sulfate.
The nature of the proteoglycan ligands at the surface of cells
stimulated by IL-3 remains a question. It is commonly accepted that the
IL-3 binding to its receptor is responsible for the association of the
latter with the common -chain of the receptor (23, 49). Based on the
absence of consensus polypeptide sequences for the biosynthesis of
chondroitin sulfate chains on the IL-3R , the latter could not be the
ligand. Therefore, it is suggested that this -chain could be part of
a molecular complex containing a highly sulfated chondroitin sulfate
proteoglycan, allowing indirect contact between IL-3R and -3R .
Furthermore, from GC/MS analysis, PGS3 has very short GAG chains (15 disaccharide units), whereas classic chondroitin sulfate proteoglycans
(including those of the other brain proteoglycans) have longer GAG
chains (more than 100 disaccharide
units).5 Therefore, it could
be suggested that the increased activity of the P33G mutein could be
related to the fact that the increased chain length of the ligand of
the mutein can favor the extracellular associations between IL-3R
receptor complexes (carbohydrate-mediated oligomerization) to induce
new signaling pathways.
The biological relevance of our findings is supported by the fact that
cells sensitive to IL-3, as mentioned above, possess a relatively high
level of disulfated chondroitin sulfate chains (although the higher
affinity ligand proposed here has not yet been identified in these
cells). A further argument comes from the brain
immunolocalization of PGS3
(50).6 Indeed, this compound
presents a preferential localization on a few neurons of the cerebellum
and the forebrain. This localization has to be related to the RT-PCR
and immunohistochemical studies showing the presence of IL-3R in the
central nervous system, with a preferential localization in large
cholinergic neurons (51-54). Because it has been demonstrated that
IL-3 has a neurotrophic effect on these neurons (increases in
acetylcholinesterase and choline-acetyltransferase), it may be
speculated that the IL-3 signaling occurs through a similar mechanism
to that described for the other interleukins (2, 44), i.e.
extracellular association of the IL-3R with a glycoconjugate ligand
(here, a chondroitin sulfate proteoglycan) due to the bifunctional
IL-3, allowing specific intracellular phosphorylation/dephosphorylation mechanisms.
 |
FOOTNOTES |
*
This work was sustained in part by a grant from the Eramus
program (to R. B.).The costs of publication of this
article were defrayed in part by the
payment of page charges. The article
must therefore be hereby marked
"advertisement" in
accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
§
To whom correspondence should be addressed. Tel.:
33-03-20-43-40-10; Fax: 33-03-20-43-65-55; E-mail:
Jean-Pierre.Zanetta@univ-lille1.fr.
Published, JBC Papers in Press, July 1, 2002, DOI 10.1074/jbc.M205282200
2
J. P. Zanetta, unpublished data.
3
V. Durier, P. Lagant, S. Kirillova, and G. Vergoten, submitted for publication.
4
J. P. Zanetta, unpublished data.
5
J. P. Zanetta, unpublished results.
6
J. P. Zanetta, unpublished results.
 |
ABBREVIATIONS |
The abbreviations used are:
CRD, carbohydrate
recognition domain;
BCIP, 5-bromo-4-chloro-3-indolyl-phosphate;
PBS, phosphate-buffered saline;
CPC, cetylpyridinium chloride;
GAG, glycosaminoglycan;
GlcA, D-glucuronic acid;
GalNAc, D-N-acetylgalactosamine;
GC/MS, gas
chromatography/mass spectrometry;
IL, interleukin;
NBT, nitro blue
tetrazolium;
GC/MS, gas chromatography/mass spectrometry;
ELISA, enzyme-linked immunosorbent assay.
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