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J Biol Chem, Vol. 273, Issue 17, 10428-10435, April 24, 1998
Identification of a Ligand Binding Site in the Human Neutrophil
Formyl Peptide Receptor Using a Site-specific Fluorescent Photoaffinity
Label and Mass Spectrometry*
John S.
Mills §,
Heini M.
Miettinen ,
David
Barnidge¶ ,
Michael J.
Vlases ,
Susan
Wimer-Mackin **,
Edward A.
Dratz¶,
Jan
Sunner¶, and
Algirdas J.
Jesaitis
From the Departments of Microbiology and
¶ Chemistry and Biochemistry, Montana State University,
Bozeman, Montana 59717-3520
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ABSTRACT |
A novel fluorescent photoaffinity
cross-linking probe,
formyl-Met-p-benzoyl-L-phenylalanine-Phe-Tyr-Lys- -N-fluorescein
(fMBpaFYK-fl), was synthesized and used to identify binding site
residues in recombinant human phagocyte chemoattractant formyl peptide
receptor (FPR). After photoactivation, fluorescein-labeled membranes
from Chinese hamster ovary cells were solubilized in octylglucoside and
separated by tandem anion exchange and gel filtration chromatography. A
single peak of fluorescence was observed in extracts of FPR-expressing cells that was absent in extracts from wild type controls. Photolabeled Chinese hamster ovary membranes were cleaved with CNBr, and the fluorescent fragments were isolated on an antifluorescein
immunoaffinity matrix. Matrix-assisted laser desorption ionization mass
spectrometry identified a major species with mass = 1754, consistent with the CNBr fragment of fMBpaFYK-fl cross-linked to
Val-Arg-Lys-Ala-Hse (an expected CNBr fragment of FPR, residues
83-87). This peptide was further cleaved with trypsin, repurified by
antifluorescein immunoaffinity, and subjected to matrix-assisted laser
desorption ionization mass spectrometry. A tryptic fragment with
mass = 1582 was observed, which is the mass of fMBpaFYK-fl
cross-linked to Val-Arg-Lys (FPR residues 83-85), an expected trypsin
cleavage product of Val-Arg-Lys-Ala-Hse. Residues 83-85 lie within the putative second transmembrane-spanning region of FPR near the extracellular surface. A 3D model of FPR is presented, which accounts for intramembrane, site-directed mutagenesis results (Miettinen, H. M., Mills, J., Gripentrog, J., Dratz, E. A., Granger,
B. L., and Jesaitis, A. J. (1997) J. Immunol.
159, 4045-4054) and the photochemical cross-linking data.
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INTRODUCTION |
The phagocyte chemotactic receptors, including the formyl peptide
receptor (FPR),1 the lipoxin
A4 receptor, the C5a receptor, the platelet-activating factor receptor, and the interleukin-8 receptor are involved in inflammation and are all members of the G protein-coupled receptor (GPCR) superfamily. Among the most studied in this inflammatory receptor family is neutrophil FPR (1). FPR binds N-formyl
peptides, such as formyl-Met-Leu-Phe (fMLF), with nanomolar affinity
(2). Such N-formyl peptides are indicators of the presence
of bacteria (3) or damage to host cell mitochondria (4, 5). Binding of
N-formyl peptides to FPR thus provides phagocytes with
signals for infection or injury and results in activation of chemotaxis and other host defensive processes including lysosomal enzyme secretion, stimulation of production of inflammatory mediators, and
generation of superoxide.
The effects of amino acid substitutions and modifications of fMLF
peptides on binding to FPR and activation have been studied extensively
(6-8). The formyl group, the methionine at position 1, and
phenylalanine at position 3 have been shown to be necessary for high
affinity binding. Decarboxylation of the C-terminal phenylalanine markedly reduces activity, but esters or amides of this residue or
peptides with C-terminal amino acid additions exhibit similar activity
to the tripeptide with the free acid. None of the fMLF functional
groups have been shown to be absolutely essential for activity but
rather they appear to individually contribute to the overall free
energy of binding.
Chemical and photoaffinity cross-linking of fMLF analogs to FPR has
been achieved by a number of groups (9-12). However, none of these
studies have identified the site of labeling. The residue in the second
position of N-formylated peptides appears to be the most
tolerant of modification (6, 13) and both of the flanking residues are
critical for high affinity binding (14); so the second residue was
chosen to accommodate the photoreactive amino acid benzoylphenylalanine
(Bpa). Bpa is chemically stable in the absence of photoexcitation, can
be directly introduced into peptide ligands by solid phase peptide
synthesis, and has been photocross-linked into several peptide
receptors (15). Here we report that a fluorescent photoaffinity analog
of fMLF, formyl-Met-p-benzoyl-L-phenylalanine-Phe-Tyr-Lys- -N-fluorescein (fMBpaFYK-fl), efficiently photocross-links to FPR residues 83-85. Derivatization of these residues in FPR by Bpa supports recent site-directed mutagenesis studies predicting that the formyl peptide binding site of FPR lies within the transmembrane spanning region, near
the transmembrane-extracellular interface of the receptor (17).
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MATERIALS AND METHODS |
Peptide
Synthesis--
fMet-p-Benzoyl-L-phenylalanine-Phe-Tyr-Lys
was synthesized from Fmoc (N-(9-fluorenyl)methoxycarbonyl)
amino acids using a Milligen 9050 peptide synthesizer and purified by
reverse phase HPLC. Peptide (4 µmol) was suspended in
dimethylformamide, 5% triethylamine, and 4 µmol of
hexanoylfluorescein-N-hydroxysuccinimide (Molecular Probes)
was added. The reaction was allowed to proceed for 5 min at 4 °C.
The products were separated by C18 reverse phase HPLC. The desired
peptide, fMBpaFYK-fl was identified by its absorbance and fluorescence
spectra (in 10 mM NaCO3, pH 10.5), and its mass
(m/z = 1340) measured by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-MS) in a
-cyano-4-hydroxycinnamic acid matrix. Samples were stored in amber
vials at 20 °C. The syntheses and all manipulations were carried
out under dim light.
Preparation of Antifluorescein-Sepharose--
Antibodies to
fluorescein isothiocyanate were prepared by injecting rabbits with
fluorescein isothiocyanate-labeled keyhole limpet hemocyanin, as
described previously (16). Serum was precipitated with 50% ammonium
sulfate and antibodies were purified on fluorescein isothiocyanate-labeled aminohexyl-Sepharose. Purified antibodies bound ~2 mol of fluorescein isothiocyanate-ethanolamine/mol of antibody, as assessed by its ability to quench fluorescein
fluorescence. The antibodies were reacted with CNBr-activated Sepharose
and cross-linked with 50 mM dimethyl pimelimidate (Pierce)
in 0.1 M Na2CO3, pH 10.5, for
16 h. The antifluorescein-Sepharose was washed extensively (>72
h) with phosphate-buffered saline, 1.5 M NaCl, and 50%
ethylene glycol. It was washed quickly (<5 min) with 1%
triethylamine, 1.5 M NaCl, 50% ethylene glycol, and
equilibrated in 10 mM HEPES (pH 7.4) and 1% octyl
glucoside just prior to use. The antifluorescein-Sepharose bound ~16
pmol of fMBpaFYK-fl per µl of Sepharose.
FACScan Binding of fMBpaFYK-fl to FPR-expressing Chinese Hamster
Ovary (CHO) Cells--
FACScan analysis was carried out as described
previously by (17). The analysis was carried out in dim light to
prevent photolysis of fMBpaFYK-fl.
Photolabeling of fMBpaFYK-fl to FPR and Preparation of CHO
Membranes--
CHO cells expressing FPR (17) or WT CHO cells were
grown in 15-cm tissue culture dishes and treated with 6 mM
sodium butyrate 16 h prior to labeling. The cells were washed 3 times with phosphate-buffered saline and incubated with 100 nM fMBpaFYKf for 5 min at 4 °C. The tissue culture
dishes were loaded directly into a Rayonet RPR-100 UV photoreactor and
exposed to UV irradiation for 15 min at 4 °C. EDTA, leupeptin, and
fMLF were added to give final concentrations of 1 mM, 1 µg/ml, and 10 µM, respectively. The cells were
harvested by scraping and centrifuged at 150,000 × g
for 30 min. The cell pellets were sonicated in phosphate-buffered
saline, 1 mM EDTA, 1 µg/ml leupeptin, 10 µM
fMLF, and 200 µM dithiothreitol (Buffer A), washed twice
with 10 mM Na2CO3, pH 10.5, 0.8 M NaCl, 1 mM EDTA, 1 µg/ml leupeptin, 10 µM fMLF, and 200 µM dithiothreitol.
HPLC Analysis of Photolabeled FPR--
Membranes from CHO cells
expressing FPR and wild type control CHO cell membranes were prepared
as described above, resuspended in 0.7 ml of Buffer A containing 3%
octyl glucoside, sonicated, and centrifuged at 150,000 × g for 30 min. The supernatant was injected onto anion
exchange (Vydac 300VHP) and gel filtration (TSK GW3000) HPLC columns
connected in series, and the columns were monitored for fluorescence
with excitation at 490 nm and emission at 520 nm. 1 ml of 1 M NaCl was injected after 60 min elution to remove material
that bound to the anion exchange column. The HPLC analysis was carried
out using a Hitachi 6200 HPLC system with a F-1050 fluorescence
detector.
Digestion of Photolabeled FPR with CNBr and Isolation of
Photocross-linked Fragments--
Photolabeled membranes from
FPR-expressing and WT CHO cells were washed with H2O, the
membranes were resuspended in 200 µl of H2O, sonicated,
and dissolved by addition of 800 µl of trifluoroacetic acid. 50 µmol of CNBr was added, and the reaction mixtures were incubated for
16 h at 20 °C. An additional 10 µmol of CNBr was added, and
the incubation continued for an additional 8 h. The samples were
frozen at 80 °C and lyophilized. The samples were resuspended in
10 mM HEPES and 1% octyl glucoside, adjusted to pH 7-8
and centrifuged at 150,000 × g for 30 min. The
supernatant was added to 30 µl of rabbit antifluorescein antibodies
bound to Sepharose and incubated for 16 h at 4 °C. The
Sepharose beads were washed 5 times with H2O, eluted with
1% triethylamine, 40% acetonitrile in water and lyophilized. For
trypsinization, the sample was resuspended in 1% octyl glucoside, 10 mM Tris, pH 8.0, and incubated with 1 µg of trypsin
(sequencing grade, Boehringer Mannheim) for 16 h at 25 °C. 4 µg of soybean trypsin inhibitor was added, followed by the addition
of 30 µl of antifluorescein immunoaffinity matrix, and the isolation
procedure described above was repeated.
GTP S Binding to FPR-expressing CHO Cells--
Membranes from
FPR-expressing CHO cells were harvested, sonicated, washed in Buffer A
and resuspended in GTP S binding buffer. Binding assays were
performed in 1 ml of 10 mM HEPES, pH 7.4, 100 mM NaCl, 1 mM Mg2+, 1 µM GDP. Samples containing 30 µg of protein were
preincubated with formyl peptide or analog at 30 °C for 10 min, 0.05 µCi of [35S]GTP S (1000 Ci/mmol) was added, and the
reaction continued for 6 min. The samples were filtered through BA 85 0.45-µm filters (Schleicher & Schuell), the filters were washed with
5 ml of 10 mM HEPES, pH 7.4, 100 mM NaCl, 1 mM Mg2+ buffer, and the bound
[35S]GTP S was measured by liquid scintillation
counting.
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RESULTS AND DISCUSSION |
The novel synthetic fluorescent photoaffinity analog fMBpaFYK-fl
activates the formyl peptide receptor more efficiently than does fMLF.
Fig. 1A shows that fMBpaFYK-fl
enhanced [35S]GTP S binding to CHO cell membranes
expressing FPR with an EC50 of 3 nM. This
EC50 was about 2-fold lower than that observed with fMLF
(EC50 ~ 6 nM). At saturation, both ligands
increased GTP S binding to a similar extent (~100% increase in
binding). Fig. 1B shows FACScan measurement of the binding
of fMBpaFYK-fl to FPR expressed in CHO cells. Analysis of the FACScan
binding data by nonlinear least squares fit of the data to a sigmoidal
curve, using Prism 2 (Graph Pad Software, Inc.), indicated that
fMBpaFYK-fl bound to FPR in intact cells with a Kd
of 37 nM. This photoaffinity analog had a binding affinity
similar to that observed with the hexapeptide,
formyl-Nle-Leu-Phe-Tyr-Nle-Lys-fluorescein, a similar fluorescent
analog of fMLF that had been previously studied (17-19).

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Fig. 1.
A, stimulation of GTP S binding to
membranes of CHO cells expressing FPR by fMLF or fMBpaFYK-fl. Membranes
isolated from CHO cells expressing FPR (17) were preincubated with the
indicated concentration of fMLF ( ) or fMBpaFYK-fl ( ), GTP S was
added, and the binding determined as described under "Materials and
Methods." The data were fit to a single binding site sigmoidal curve
and EC50s were determined using Graph Pad Prizm 2. B, binding of fMBpaFYK-fl to FPR. CHO cells expressing the
formyl peptide receptor (17) were incubated with the indicated
concentrations of fMBpaFYK-fl in phosphate-buffered saline and 5%
fetal calf serum in the presence ( ) or absence ( ) of 10 µM fMLF for 1 h at 4 °C. Cell-associated
fluorescence was determined by FACScan analysis. The data were fit to a
single binding site sigmoidal curve, and the Kd was
determined using Graph Pad Prizm 2.
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UV irradiation of FPR occupied with fMBpaFYK-fl, produced extensive
nonreversible binding of the photoactivatable ligand, as shown in Fig.
2. After 10 min of irradiation, greater
than 40% (n = 2) of the fMBpaFYK-fl was no longer
displaced from FPR by fMLF under conditions that completely displaced
fMBpaFYK-fl, which had not been exposed to UV light.

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Fig. 2.
Specific fluorescent photoaffinity labeling
of FPR by fMBpaFYK-fl. CHO cells expressing FPR were incubated for
10 min with 40 nM fMBpaFYK-fl, and the cells were exposed
to UV light for the indicated time. A 1000-fold excess of fMLF was then
added, the cells were incubated at 4 °C for 60 min, and the amount
of analog bound to the cells was determined using FACScan analysis
(17). No photolabeling was observed when photoirradiation was carried
out in the presence of a 1000-fold molar excess of fMLF. The 100%
photocross-linking level was defined as the amount of fMBpaFYK-fl bound
with no added fMLF and no UV exposure.
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To determine if fMBpaFYK-fl specifically photolabeled FPR, octyl
glucoside-solubilized membranes from CHO cells expressing FPR or WT
control CHO cells, which had both been exposed to fMBpaFYK-fl and UV
irradiated, were injected onto anion exchange and gel filtration HPLC
columns connected in series. The columns were monitored for fluorescein
fluorescence (excitation 490 nm/emission 520 nm). 1 ml of 1 M NaCl was injected at time = 60 min to remove
material that bound to the anion exchange column and subject that
material to size separation by gel filtration. Fig.
3 shows a large peak of fluorescein
labeled protein from FPR-expressing CHO cells that was not retained by
the anion exchange column (consistent with an isoelectric point of 9.4 for FPR calculated from its amino acid sequence). This peak was found
to FPR by Western blot (not shown) and was completely absent in the WT
controls, indicating that the fMBpaFYK-fl was specifically labeling
FPR. The area under the FPR peak in Fig. 3 represented 60-70% of the
eluted fluorescein fluorescence and indicated that most of the
photolabeled material was in FPR.

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Fig. 3.
Analysis of fMBpaFYK-fl photolabeling to FPR
by tandem anion exchange gel filtration HPLC. Octyl
glucoside-solubilized membranes from fMBpaFYK-fl-photolabeled CHO cells
expressing FPR or wild type CHO control cells were prepared as
described under "Materials and Methods" and injected onto tandem
anion exchange gel filtration HPLC columns pre-equilibrated in 10 mM HEPES, pH 7.4, 50 mM sodium acetate, 1%
octyl glucoside, and eluted at a flow rate of 0.5 ml/min. The columns
were monitored for fluorescence with excitation at 490 nm and emission
at 520 nm. 1 ml of 1 M NaCl was injected at time = 60 min. This eluted proteins that bound to the anion exchange column
directly into the gel filtration column and these bound proteins were
then separated by gel filtration. The integrated area under the FPR
peak represented 50-70% (range of 3 determinations) of the total
fluorescein fluorescence eluting from the columns.
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To determine the site of photocross-linking between fMBpaFYK-fl and
FPR, photolabeled FPR was cleaved with CNBr and the
fMBpaFYK-fl-containing adducts were identified by MALDI mass
spectrometry. Fig. 4 shows a model of the
transmembrane topology of FPR (17) where the positions of the
methionine CNBr cleavage sites are indicated by gray
shading. The table inset shows the expected masses of the 11 possible cross-linked adducts between CNBr-digested FPR and
benzoylphenylalanine-FYK-fl (BpaFYK-fl), the CNBr cleavage product of
fMBpaFYK-fl. All of the expected masses of the CNBr cleavage products
are sufficiently different that they can be resolved by MALDI-MS, which
has a mass accuracy of about 0.1%.

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Fig. 4.
Schematic representation the CNBr cleavage
sites in FPR. The positions of transmembrane helices I and III-VII
were based on the findings of Baldwin (44), and the position of helix
II is based on the findings of Miettinen et al. (17).
Residues with heavier black circular outlines are those that
have previously been shown to affect ligand binding (17). The
methionine CNBr cleavage sites are indicated with a gray
background. Residues with white letters on a
black or gray background indicate the region
identified as the site of cross-linking with fMBpaFYK-fl. Residues with
white letters on a black background are those
residues that are found in the cross-linked fragment following both
CNBr and trypsin cleavage. The inset table shows the
expected masses of the CNBr fragments of FPR cross-linked with the CNBr
cleavage product of fMBpaFYK-fl.
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Since the HPLC analysis indicated that most of the photoaffinity label
was incorporated into FPR, CNBr digestions were performed directly on
CHO cell membranes to maximize the yield of photocross-linked peptides.
To obtain sufficient photolabeled FPR for identification of CNBr
fragment adduct(s) by MALDI-MS and to show that these adduct(s) were
derived from FPR, 20 15- × 1-cm tissue culture plates from WT CHO
cells and CHO cells expressing FPR were photolabeled with 100 nM fMBpaFYK-fl. Membranes from an equal number of cells of
each type were solubilized in 1 ml of 80% trifluoroacetic acid and
cleaved with CNBr.
Fluoresceinated Adducts from Both Wild Type and FPR-expressing CHO
Cell Membranes--
Fluoresceinated adducts from both wild type and
FPR-expressing CHO cell membranes were isolated with antifluorescein
immunoaffinity chromatography, as described under "Materials and
Methods." 20 and 8 pmol of cross-linked fluoresceinated peptides were
isolated from FPR-expressing and WT CHO cell membranes, respectively,
indicating that ~60% (i.e. 12 of 20 pmol total) was
specifically photocross-linked to FPR, in agreement with the HPLC
analysis shown in Fig. 2. The material eluted from the antifluorescein
antibodies was analyzed by MALDI-MS (Fig.
5, inset). Mass spectra
obtained from WT cells was subtracted from that observed for
FPR-expressing cells, and a typical difference spectrum is shown in
Fig. 5.

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Fig. 5.
MALDI difference spectrum of fMBpaFYK-fl
cross-linked to FPR. fMBpaFYK-fl cross-linked to CHO cells
expressing FPR or wild type CHO cells were cleaved with CNBr and
isolated as described under "Materials and Methods." The samples
were resuspended in 0.1% trifluoroacetic acid, 50% acetonitrile, an
equal volume of saturated -cyano-4-hydroxy cinnamic acid in 0.1%
trifluoroacetic acid, 50% acetonitrile was added; the samples were air
dried and analyzed by MALDI-MS. The background spectrum seen with wild
type CHO cells was subtracted from the spectra observed with
FPR-expressing CHO cells. Three major peaks were observed at 1182, 1754, and 1913 Da, which corresponded to the expected masses of
BpaFYK-fl (1182), BpaFYK-fl-Val-Arg-Lys-Ala-homoserine (1755), and
fMBpaFYK-fl (i.e. uncleaved peptide) cross-linked to
Val-Arg-Lys-Ala-homoserine (1913). The position of
Val-Arg-Lys-Ala-homoserine in FPR is indicated in Fig. 4. Upper
inset, MALDI-MS of fMBpaFYK-fl cross-linked to CHO cells
expressing FPR; lower inset, MALDI-MS of fMBpaFYK-fl
cross-linked to WT CHO cells.
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Three major mass peaks were observed at 1182, 1754, and 1913 Da (see
Fig. 6B for an expanded view
of the difference spectrum). These values corresponded to the expected
masses of BpaFYK-fluorescein (1182), BpaFYK-fl cross-linked to the FPR
CNBr peptide Val-Arg-Lys-Ala-Hse (1755), and fMBpaFYK-fl
(i.e. the uncleaved peptide) cross-linked to the FPR peptide
Val-Arg-Lys-Ala-Hse (1913). The mean mass difference between cleaved,
uncross-linked agonist peptide and the cross-linked and cleaved peptide
was 573 ± 1, which is the mass of the FPR CNBr peptide
Val-Arg-Lys-Ala-Hse (FPR residues 83-87). The average mass difference,
representing the FPR cross-linking site, was determined from four
separate CNBr cleavage reactions of cross-linked FPR, and the same mass
peaks at m/z at ~1182, 1755, and 1913 were observed in all four CNBr
cleavage reactions.

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Fig. 6.
MALDI-MS analysis of CNBr and tryptic digests
of fMBpaFYK-fl and its cross-linked adducts to FPR. A,
fMBpaFYK-fl was cleaved with 10 mM CNBr in 80%
trifluoroacetic acid, and 16 pmol were analyzed as described in Fig. 5.
B, MALDI spectrum from Fig. 5 on an expanded scale.
C, fMBpaFYK-fl was cross-linked to FPR-expressing CHO cells,
cleaved with CNBr, and subsequently cleaved with trypsin, and analyzed
by MALDI as described under "Materials and Methods" and the legend
to Fig. 5. The x axes of panels B and
C were offset 573 (mass of Val-Arg-Lys-Ala-Hse) and 401 (mass of Val-Arg-Lys) Da, respectively, to align with the CNBr cleavage
intermediates of fMBpaFYK-fl seen in panel A.
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To confirm that the FPR sequence Val-Arg-Lys-Ala-Hse was the
fMBpaFYK-fl photocross-linking site, peptides from the antifluorescein eluate were further cleaved with trypsin, purified using
antifluorescein antibodies, and subjected to MALDI mass spectrometry.
After trypsinization, a major mass peak of 1582 was observed (Fig.
6C) indicating a cross-linked FPR fragment of 400 Da, very
similar to the expected mass of Val-Arg-Lys (expected mass 401, FPR
residues 83-85). Fig. 6 shows a comparison of the mass spectra of
fMBpaFYK-fl cleaved with 10 mM CNBr (Fig. 6A) to
the CNBr cleavage product of fMBpaFYK-fl cross-linked to FPR (Fig.
6B) and fMBpaFYK-fl cross-linked to FPR cleaved with both
CNBr and trypsin (Fig. 6C). The mass axes of Fig. 6,
B and C have been shifted by 573 and 401 Da,
which are the masses of Val-Arg-Lys-Ala-Hse and Val-Arg-Lys,
respectively, to align them with the masses of the CNBr cleavage
products of fMBpaFYK-fl. The cross-linked products in Fig. 6,
B and C both show the intermediates of incomplete
cleavage of fMBpaFYK-fl by CNBr as also seen in Fig. 6A.
These additional cross-linked fragments serve as fingerprints of
fMBpaFYK-fl cross-linking and provide additional mass spectral peaks,
which are characteristic of the agonist peptide and can thus be used to
support the identification of cross-linked peptides.
Three-dimensional Placement of the fMLF Binding Site in
FPR--
The ability to photoaffinity cross-link FPR with a high
affinity analog of fMLF provides an opportunity to experimentally test
the intramembrane ligand binding hypothesis for G protein-coupled peptide receptors (17, 18). A three-dimensional model of FPR was
generated from a rhodopsin template designed by Herzyk and Hubbard
(20), and a space filling model of fMet-Bpa-Phe (fMBpaF) was placed
between the seven transmembrane helices (Fig.
7). Two stereo views are shown in Fig. 7,
a view from the extracellular space and a transmembrane view. fMBpaF
was positioned between the helices to allow maximum contact with
residues previously shown to be important in ligand binding (17). By
modeling fMBpaF in an extended conformation, the Bpa moiety could be
placed near the site of cross-linking while maintaining interactions
between fMBpaF and residues that affect binding. The methionine and
phenylalanine side chains of fMBpaF, which are essential for high
affinity binding, were positioned deep within the binding pocket
(relative to the extracellular side), whereas the Bpa side chain was
positioned nearer the extracellular space, so as to be consistent with
the cross-linking data. Since studies with model compounds suggest the
carbonyl carbon of the benzophenone moiety of Bpa generally reacts with
another carbon within a distance of approximately 3 Å and the carbon
adjacent to the amino group of lysine is reported to be one of more
reactive side chains toward photocross-linking with benzophenone (15),
the carbon of Lys-85 was placed within 3 Å of the carbonyl oxygen
of the benzophenone moiety of fMBpaF. In this position, the amine
nitrogen of Lys-85 (II-24) is within 2-3 Å of the methionine carbonyl
oxygen on fMBpaF, sufficiently close to form a hydrogen bond.
Alternatively, Lys-85 could ion pair with Asp-284 and still be close
enough to the carbonyl oxygen of the benzophenone moiety of fMBpaF to
photocross-link effectively. In the present model, neither of the
sidechains of Val-83 or Arg-84 appear to be sufficiently close to the
benzophenone carbonyl of fMBpaF to be likely sites of cross-linking,
but their backbone moieties might be close enough to cross-link
efficiently. The present data does not distinguish between
cross-linking to the three residues (83-85), and additional studies
will be needed to delineate the exact site(s) of interaction.

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Fig. 7.
A three-dimensional model of FPR. Upper
panel, Stereo view of FPR model with bound fMBpaF as viewed from
the extracellular space. Lower panel, stereo transmembrane
view of the model with helices V-VII in the foreground. Helices are
colored: I, blue; II, magenta; III,
aqua; IV, yellow; V,
orange-red; VI, light blue; and VII,
orange. The transmembrane segments of FPR were selected
based on the multiple sequence alignment of G protein-coupled receptors
(GPCRs) by Baldwin (44), except that helix II was assigned to residues
61-87 to be consistent with previous site-directed mutagenesis of FPR
(17) and the photocross-linking data presented in this paper. The
starting model was generated using the automated rule-based method
described by Herzyk and Hubbard (20) by submitting the FPR helix
segments I-VII to their GPCR modeling site
(Expasy.hcuge.ch/CAI-bin/Promod-GPCR.pl). Rhodopsin, which has a
high sequence homology to FPR, was used as the template. A space
filling model of gray) was placed between the seven
transmembrane helices so as to be consistent with evidence from
site-specific mutagenesis (17). The plane of the phenyl ring of the
peptide ligand was positioned parallel to the long axes of the helices
to allow fMBpaF to fit between the helices. Adjustments were made to
the model based on our photocross-linking data as follows: Lys-85
(K85) was positioned so that the amino group was within
hydrogen bonding distance of the methionine carbonyl of fMBpaF, and the
benzophenone moiety of fMBpaF was rotated at the carbon of
benzoylphenylalanine to position it within 0.3 nM of the
side chain of Lys-85. The sidechains of FPR Val-83 (V83),
Arg-84 (R84), Lys-85 (K85), and Asp-284
(D284) are represented as CPK space filling models with
carbon green, hydrogen white, nitrogen
blue, and oxygen red. An asterisk is
placed close to the benzophenone carbonyl oxygen photocross-linking
site, which is colored red.
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We have previously shown that mutation of FPR Leu-78 (II-17; helix II,
residue 17 from the N terminus of the helix) or Phe-291 (VII-11) to Ala
markedly reduced ligand binding (17). These residues are 2 helical
turns toward the cytoplasmic side of the membrane from Lys-85 (II-24)
and Asp-284 (VII-4), respectively. Table
I shows the sequences of the residues of
human FPR surrounding Lys-85 (II-24) and Asp-284 (VII-4) aligned with
the analogous residues of rabbit, mouse, gorilla, and macaque FPRs.
Also shown are the homologous sequences of other closely related
chemotactic GPCR's; lipoxin A4 receptor (LPXA4R), C5a receptor,
interleukin 8 and 8A receptors (ILA8R and ILA8AR) and a human
coreceptor for HIV (CCR5). These receptors either have Lys at position
II-24 and Asp at position VII-4 (underlined in Table I) or
they lack both Lys and Asp at these positions. The correlation in
occurrence of these two residues suggests that they might interact in
the structure, possibly by forming an ion pair. This ion pair might be
similar to the putative ion pair between Glu-113 (III-3) and Lys-296
(VII-11) in opsin (21) or Asp-103 (III-7) and Lys-331 (VII-4) in the
1B adrenergic receptor (22). Both of these putative ion
pairs are thought to be important in maintaining these receptors in
their inactive conformation, since mutation of either of the residues
involved in the ion pairs results in constitutively active receptors
(21, 22). Both human and rabbit FPRs bind fMLF with high affinity and
both contain Lys at position II-24 and Asp at position VII-4, whereas
mouse FPR, human LXA4R, and human FPRL2 bind fMLF with much
lower affinity, and these three receptors all lack both Lys at position
II-24 and Asp at position VII-4 (23-25). If, in fact, Lys-85 and
Asp-284 do form an ion pair in FPR and ligand binding serves to disrupt
such pairing, then Lys-85 might be positioned well to interact with the
benzophenone carbonyl as is shown in Fig. 7.
View this table:
[in this window]
[in a new window]
|
Table I
Alignment of sequences of representative chemotactic receptors near the
extracellular interfaces of helix II and helix VII
|
|
Previous studies with other GPCR have implicated analogous regions of
the putative second transmembrane spanning region as being important in
ligand binding. Site-directed mutagenesis of the neurokinin-1 and
neurokinin-2 receptors identified four residues in the putative second
transmembrane helix as important in the binding of substance P and
neurokinin A, respectively, to these receptors (26, 27). One of the
residues identified as important in ligand binding in the two
receptors, Tyr-92 (Tyr-93), is analogous to Lys-85 in FPR, is the
most likely ligand cross-linking site in FPR in our experiments.
Another residue important for ligand binding in the two receptors,
Asn-85 (Asn-86), is analogous to Leu-78 in FPR. The neuropeptide Y
receptor also contains a Tyr in an analogous position to Lys-85 in FPR.
Mutation of this residue to Phe substantially reduced the binding of
neuropeptide Y to the neuropeptide Y receptor suggesting that the OH
group of Tyr makes an important hydrogen bond with ligand (28). The
lutropin/chorionic gonadotropin receptor has also been analyzed at the
analogous position in helix II (29). In the lutropin/chorionic
gonadotropin receptor case, mutation of Asp in this position to Lys did
not alter ligand affinity, but completely blocked ligand activation of
adenylate cyclase. A complimentary mutation of a Lys residue in the
normal peptide ligand (Lys Asp) resulted in a ligand which would
activate the Asp Lys receptor mutant but not the WT or the
Asp Ala receptor mutant. This was strong evidence that a
complementary interaction between ligand and the receptor residue in
the position analogous to Lys-85 in FPR was essential for receptor
activation.
Evidence for the location of the ligand binding sites of many GPCR has
been provided using site-directed mutagenesis. However, very few of
these sites have been analyzed directly by ligand cross-linking. An
important residue in the binding site of the adrenergic receptor
was identified as Trp-330 (VII-8) by photoaffinity labeling with
iodocyanopindolol-diazirine (30). A chemically reactive muscarinic
agonist cross-linked to the m1 muscarinic receptor at residue Asp-105
(III-7) (31). Both of these sites, as is the case for the ligand
binding site of FPR, map to transmembrane regions near the
extracellular face of these receptors. The ligand binding sites on FPR,
the adrenergic receptor, and the muscarinic receptor, all map to a
region very similar to that found for the retinal binding site of
rhodopsin (32-43). Therefore, we conclude that the binding sites for
many different types of GPCR ligands appear to reside in a very similar
region of GPCR within the transmembrane region near the extracellular
face of the membrane.
 |
ACKNOWLEDGEMENTS |
We gratefully acknowledge Pawel Herzyk and
Rod E. Hubbard for establishing the 7TM receptor modeling program at
Swiss Pro on the World Wide Web
(Expasy.hcuge.ch/CAI-bin/Promod-GPCR.pl).
 |
FOOTNOTES |
*
This work was supported in part by National Science
Foundation EPSCoR Grant RII-891879 (to E. A. D.), a Grant from the
Pittsburgh Supercomputing Centers through the National Institutes of
Health resource Grant 2p41RR06009, a grant from the Rocky Mountain
Chapter of the Arthritis Foundation and the Harmon Foundation (to
J. S. M.), a grant from the Rocky Mountain Chapter of the Arthritis
Foundation (to H. M. M.), and Public Health Service Grants
1RO1A40108-01 and RO122735 (to A. J. J.).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: Montana State
University, Dept. of Microbiology, 109 Lewis Hall, Bozeman, MT
59717-3520. Tel.: 406-994-6506; Fax: 406-994-4926; E-mail:
umbmj{at}gemini.oscs.montana.edu.
Present address: Dept. of Analytical Chemistry, Uppsala
University, Box 531, S-751 21 Uppsala, Sweden.
**
Present address: Combined Program in Pediatric Gastroenterology and
Nutrition, Enders Bldg. 1209, Children's Hospital, 300 Longwood Ave.,
Boston, MA 02115.
1
The abbreviations used are: FPR, formyl peptide
receptor; fMBpaFYK-fl,
formyl-Met-p-benzoyl-L-phenylalanine-Phe-Tyr-Lys- -N-fluorescein; GPCR, G protein-coupled receptor; fMLF, formyl-Met-Leu-Phe; Bpa, benzoylphenylalanine; HPLC, high performance liquid chromatography; MALDI-MS, matrix-assisted laser desorption ionization mass
spectrometry; CHO, Chinese hamster ovary; WT, wild type; FACScan,
fluorescence-activated cell scanner.
 |
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