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National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709;
New York University School of Medicine, New York, NY 10016; and
Research Center for AIDS and HIV infection, New York Harbor Veterans Affairs Medical Center, New York, NY 10010
| Abstract |
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| Introduction |
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500 amino acids with varying
numbers of attached high mannose and complex-type oligosaccharides
(3). From sequence comparisons of different
immunodeficiency viruses of primates, five conserved regions (C15)
and five regions with variable amino acid sequences (V15) have been
identified in HIV-gp120. Disulfide bonds lead to the formation of
complex loop structures of the first four variable domains
(4). Discontinuous regions of the constant domains are
important for the interaction of HIV-gp120 with the transmembrane
protein HIV-gp41, and with the primary receptor of HIV, CD4
(5). Intense interest has been focused on HIV-gp120, because this glycoprotein is the main target of HIV neutralizing Abs (6). Considerable attention has been paid to Abs specific to the third variable loop of HIV-gp120, which contains the so-called "principle neutralizing domain" (7, 8), and to the CD4 binding region. Many of these Abs have high affinity and potent neutralizing abilities for laboratory adapted strains; however, they often lack neutralizing abilities for primary isolates.
Primary isolates, which may have been cultured in PBMC but have not been passaged in cell lines, are closely related to the viruses occurring during natural infection. Several human mAbs specific for various regions of HIV-gp120 have been reported to have potent neutralizing activity against primary isolates (9, 10). Passive immunization of SCID-human mice with human mAbs provided protection against infection with primary isolates (11). However, escape variants of the virus have been isolated, which emphasizes the need for combinations of Abs with different specificities (12).
Elucidation of the epitopes that these Abs recognize can be an important part of the development of HIV vaccines. Furthermore, it can provide insights into the tertiary structure of HIV-gp120 (13), because x-ray analysis of only a truncated HIV-gp120 molecule is available (5). Several methods for the characterization of epitopes have been described, such as random phage epitope library screening, x-ray analysis, proteolytic footprinting, and epitope excision/extraction techniques. Random phage epitope library screening was used for the identification of peptide sequences, which were capable of interacting with anti-HIV-gp120 Abs (14, 15). X-ray analysis was used successfully for the elucidation of epitopes (16). However, this method is time consuming, because of difficulties associated with protein crystallization.
Proteolytic footprinting methods are based on the protection of residues in the Ag that are involved in affinity binding against proteolysis or chemical modification and the high resistance of the Ab to proteolytic digestion (17, 18). In epitope excision methods, the protein of interest is complexed with the Ab and then digested enzymatically. Only fragments that are protected by the Ab remain affinity bound and can be identified. Because the Ag is bound to the Ab in its native conformation under physiological conditions, this approach allows the identification and characterization of linear and discontinuous epitopes. In epitope extraction, the Ag of interest is first digested enzymatically and subsequently passed over immobilized Ab beads. Recently, epitope excision/extraction techniques have been used in combination with matrix-assisted laser desorption (MALDI)3-time of flight (TOF) mass spectrometry for the characterization of linear epitopes of the HIV proteins HIV-p24 and HIV-gp120 (19, 20).
We report here the elucidation of a discontinuous epitope in the HIV envelope protein HIV-gp120, recognized by the mAb 1331A by epitope excision/extraction techniques followed by MALDI-TOF mass spectrometry. 1331A is a human mAb specific to the C5 region of HIV-gp120, which has been produced from PBMC of an HIV-infected patient, as described previously (21, 22). Binding studies of intact virus particles of HIV revealed a high affinity of 1331A to laboratory-adapted strains and primary isolates (23). These studies also demonstrated that the epitope recognized by 1331A Ab is highly conserved and well exposed on HIV.
| Materials and Methods |
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Recombinant HIV-gp120 from HIV-1 strain SF-2 was obtained from Austral Biologicals (San Ramon, CA). It was produced by secretion from Chinese hamster ovary cells, purified by ion exchange chromatography followed by gel filtration chromatography, dissolved in PBS (0.14 M NaCl, 2.7 mM KCl, 4.3 mM Na2HPO4, 1.5 mM KH2PO4, pH 7.2), 1 mM EDTA, and 1 mM EGTA, pH 7.4, and stored at -20°C. The human mAb 1331A (subclass IgG3) was produced as described previously (21, 22). The Ab solution was stored at -20°C. The synthetic peptides were received from Genosys Biotechnologies (The Woodlands, TX). Endoproteinases Glu-C and Asp-N were purchased from Sigma (St. Louis, MO), trypsin-(tosylamido-2-phenyl)ethylchloromethyl ketone-treated (TPCK) was obtained from Worthington Biochemical (Freehold, NJ), and endoproteinase Lys-C was obtained from Wako Chemical (Dallas, TX). Aminopeptidase M and carboxypeptidase Y were obtained from Sigma.
MALDI-TOF mass spectrometry
MALDI-TOF mass spectra were acquired on a Voyager-RP MALDI-TOF
mass spectrometer (Perseptive Biosystems, Framingham, MA), equipped
with a nitrogen laser (
= 337 nm). The matrix used was
-cyano-4-hydroxycinnamic acid (Aldrich, Milwaukee, WI). It was
recrystallized in hot methanol, stored in the dark, and before sample
analysis a fresh saturated solution of the matrix in
water/ethanol/formic acid 45/45/10 (v/v) was prepared. One-half
microliter of the sample was mixed with 0.5 µl of the matrix solution
and dried at room temperature. One hundred twenty-five laser shots were
summed per sample spectrum. Two standard proteins were used for
external calibration in the desired mass range.
Immobilization procedure
Cyanogen bromide (CNBr)-activated Sepharose beads (0.1 g) were suspended in 5 ml of 1 mM HCl and incubated for 15 min. After washing the beads with 1 mM HCl followed by 0.1 M NaHCO3 coupling buffer, the Ab (20 µg) was added to the beads and incubated for 2 h at room temperature with slow rotation. The beads with the now covalently attached Ab were subsequently washed with 0.1 M Tris-HCl, pH 8.0. Unreacted groups on the CNBr Sepharose were blocked by incubation with 0.1 M Tris-HCl, pH 8.0, for 2 h. The beads were washed successively with a 0.1 M sodium acetate, 0.5 M NaCl, pH 4.0, buffer and a 0.1 M Tris-HCl, pH 8.0, buffer. The beads were subsequently equilibrated in PBS and incubated for 2 h at room temperature with and without HIV-gp120. After washing the beads with PBS, an aliquot of the suspension was removed for MALDI-TOF analysis. Epitope excision and extraction experiments were performed as previously described (19). For epitope excision, the beads were resuspended in 50 mM NH4CO3, pH 7.8, and digested with Asp-N (1:20 enzyme:substrate ratio) at 37°C for 12 h. The beads were then washed with the digestion buffer and an aliquot was removed for MALDI-TOF analysis. The fragment that remained affinity bound was digested successively with endoproteinases Glu-C and Lys-C for 12 and 6 h, in 50 mM NH4CO3 buffer, pH 7.8, and PBS, pH 7.2, respectively. The beads were washed with the digestion buffer, and an aliquot was removed for MALDI-TOF analysis.
The affinity-bound peptides were further digested with the exopeptidases aminopeptidase M and carboxypeptidase Y. For aminopeptidase digestion, the beads with the affinity-bound peptides were equilibrated in 100 mM phosphate buffer, pH 7.2. The enzyme was added in an enzyme:substrate ratio of 1:10 and incubated at 37°C with gentle rotation for 1272 h. For digestion with carboxypeptidase Y, the beads with the affinity-bound peptide were incubated with carboxypeptidase (1:20 enzyme:substrate ratio) in 50 mM N-methylmorpholine buffer, pH 7.2, at 37°C for 14 h with slow rotation. After washing three times with the digestion buffer, an aliquot of the beads was removed for MALDI-TOF analysis.
| Results |
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To define the epitope that the 1331A Ab recognizes in the intact
HIV-gp120 molecule, the Ab was first immobilized on CNBr Sepharose
beads and was incubated with HIV-gp120 from HIV-1 strain SF-2. The
beads were subsequently analyzed directly by MALDI-TOF mass
spectrometry. The MALDI-TOF mass spectrum of HIV-gp120 affinity bound
to immobilized 1331A Ab on CNBr Sepharose beads is shown in Fig. 1
. No affinity-bound proteins were
observed in a control experiment without previous incubation with
HIV-gp120. The molecular mass of affinity-bound HIV-gp120 was found to
be approximately m/z 100 kDa. A theoretical
average molecular mass of 57,496 Da can be calculated from the amino
acid sequence of HIV-gp120, shown in Fig. 2
(24). The differences in
the detected and the predicted molecular mass are due to the high
glycosylation of HIV-gp120. These data are consistent with the
molecular mass previously determined by MALDI-TOF mass spectrometry and
SDS-PAGE (20, 25). As observed previously, this HIV-gp120
preparation lacks the terminal two amino acids, K-508 and R-509
(20). Furthermore, the C terminus is heterogeneous with
truncation residues E507, R506, Q505-V504, and V503 having been
observed (20).
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To define the epitope recognized by the 1331A mAb, affinity-bound
HIV-gp120 was then digested with endoproteases. After treatment of the
Ab-Ag complex with endoproteinase Asp-N, one fragment of
m/z 3989 was found to remain affinity bound (Fig. 3
). The molecular mass of this fragment
is in good agreement with the theoretical average molecular mass
of the C-terminal peptide 475507 of HIV-gp120:
DNWRSELYKYKVIKIEPLGIAPTKAKRRVVQRE (3986 Da), as calculated from its
amino acid sequence. Interestingly, no truncated peptides remained
affinity bound to the 1331A Ab. Peptide 475507, affinity bound to
1331A Ab, was digested further with endoproteinase Glu-C. Fig. 4
shows the MALDI spectrum of the peptide
of m/z 3200, which remained affinity bound to the
immobilized 1331A Ab after Glu-C digestion. This corresponds to the
theoretical average molecular mass of the peptide 481507 of
HIV-gp120: LYKYKVIKIEPLGIAPTKAKRRVVQRE (3198 Da). Attempts to
characterize the epitope further by digestion for 6 h with
endoproteinase Lys-C, which has five potential cleavage sites in this
fragment, led to complete loss of affinity binding. In the supernatant
of the digest, two peptides with m/z 1038 and
m/z 942 were identified, corresponding to
peptides IEPLGIAPTK (amino acids 489498, 1038 Da) and RRVVQRE (amino
acids 501507, 942 Da) of HIV-gp120 (data not shown).
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To test if peptide 481507 shows different behavior when
extracted from solution, HIV-gp120 was digested 36 h with
endoproteinase Glu-C and subsequently passed over immobilized 1331A
beads. Only one peptide was observed to remain affinity bound (Fig. 6
) after epitope extraction of the Glu-C
digest of HIV-gp120. This peptide, with a mass of
m/z 3200, corresponded to peptide 481507 of
HIV-gp120. As observed in the epitope excision experiments, no
truncated peptides bound to the Ab from solution. Digestion of the
affinity-bound peptide with exoproteinase aminopeptidese M led again to
digestion up to V486. Subsequent Lys-C digestion for 6 h resulted
again in loss of affinity binding (data not shown).
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| Discussion |
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In this study, we describe the mapping of the epitope recognized by the 1331A Ab, using proteolytic digestions of the HIV-gp120/1331A complex followed by MALDI-TOF mass spectrometry. Digestions with endoprotease Glu-C of HIV-gp120 affinity bound to immobilized 1331A Ab resulted in one affinity-bound peptide, LYKYKVIKIEPLGIAPTKAKRRVVQRE (amino acids 481507), which contains the strongly immunogenic region APTKAKRRVVQRE. Because E507 cannot be cleaved with carboxypeptidase Y, and HIV-gp120 with deleted E507 does not bind to the Ab, E507 must be involved in the affinity binding with the 1331A Ab. Assuming that the epitope is linear, Lys-C digestion, which has five potential cleavage sites in this fragment, should result in fragments YKVIKIEPLGIAPTKAKRRVVQRE (482507, 2779 Da), VIKIEPLGIAPTKAKRRVVQRE (486507, 2488 Da), IEPLGIAPTKAKRRVVQRE (489507, 2148 Da), AKRRVVQRE (499507, 1141 Da), or RRVVQRE (501507, 942 Da), depending on the length of the epitope. However, Lys-C digestion results in loss of binding to the Ab. These data indicate that one or more of the lysine residues within the peptide 481507 are not protected by the Ab. When this (or these) sites are cleaved by endoproteinase Lys-C, affinity is lost. These results are consistent with a discontinuous and/or conformational epitope. Cleavage with aminopeptidase M was observed only up to V486, which is different from the results of a previous study of a polyclonal goat Ab preparation specific to the C5 region of HIV-gp120, where cleavage was observed up to E-490 (20). An epitope extraction experiment was performed to determine whether any peptides can be extracted from a digest of HIV-gp120 with endoproteinase Glu-C. Surprisingly, peptide 481507 could be extracted from solution, and subsequent enzymatic digestions with aminopeptidase M and Lys-C led to results very similar to those from the epitope excision experiments. Epitope extraction experiments with C-terminal truncated peptides revealed that residue I-487 is essential for affinity binding of the peptides. We conclude from these experiments that amino acids of two noncontinuous regions are involved in binding to 1331A Ab, E-507 and I-487.
Interestingly, I-487 and E-507 are located on opposite sides of a
hydrophobic pocket (Fig. 8
), which was
postulated from computer modeling and sequence comparisons
(31). It has been proposed that this pocket is important
for interaction with the 5-aa cysteine-linked loop of HIV-gp41
(31, 32). Mutations of amino acids in the sequence
IEPLGVAPT (amino acids 489497) resulted in a nearly complete loss of
the affinity of HIV-gp120 for HIV-gp41 (33). Although
x-ray analysis of HIV-gp120 in complex with the CD4 receptor and a mAb
has been determined, structural information from x-ray analysis about
the extreme C terminus is still missing, because a truncated HIV-gp120
preparation was used in this study (5). Recently, the
mouse mAb 80315.6 that is specific to the amino acids APTKAKR (amino
acids 495501) of HIV-gp120 was described. The affinity of this Ab to
the native HIV-gp120 and synthetic peptides was evaluated to obtain
further structural information about the tertiary structure of this
region. HIV-gp120 and the synthetic peptides had comparable affinity
for the Ab. Because the peptides had a low percentage of
helices in
solution, a disordered conformation of the same sequence in the native
HIV-gp120 molecule was proposed (13). However, the mAb
used by Ferrer et al. is of murine origin induced by immunization with
recombinant HIV-1 gp120, and therefore the structural information
obtained may not reflect the conformation of HIV-gp120 in the intact
virus particle. In the present study, we used a human mAb, and observed
a discontinuous epitope involving amino acids I-487 and E-507 of
HIV-gp120. These data support the loop structure predicted by the
molecular modeling studies. Similar to 1331A, the mouse mAb M38 was
mapped to two noncontinuous stretches of amino acids flanking both
sides of the loop: KYK (amino acids 483485) and KAKR (amino acids
498501) (34).
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MALDI-TOF mass spectrometry has been used for the rapid characterization of linear epitopes. Proteolytic digestion of the Ag was followed by immunoprecipitation with the Ab and mass spectrometric characterization of the antigenic peptides (38). Epitope excision of the affinity-bound Ag in combination with MALDI-TOF mass spectrometry was used for the characterization of linear epitopes (19, 20). We report here the first application of this method to a discontinuous epitope. Advantages of epitope excision/extraction methods in combination with MALDI-TOF mass spectrometry are their low time consumption and that the enzymatic digestions are performed with the native protein, which allows the identification of discontinuous epitopes. This method can provide information impossible to obtain from mapping studies with peptide ELISAs. While such ELISA methods can sometimes demonstrate reactivity with peptides of 68 aa, increased affinity is observed when the epitope is determined using the complete molecule. For example, the identification of additional regions, which are involved in affinity binding, can explain the differences observed between the affinities of a synthetic peptide and native HIV-gp120 for the human mAb 694/98-D (28). Furthermore, the data obtained in this study may explain why two anti-C5 human mAbs, 858-D and 989-D, by ELISA map to the same core epitope, but by immunofluorescence on HIV-infected cells show different clade specificities (29).
Elucidation of epitopes in HIV-gp120 recognized by the human immune system is crucial for a better understanding of the antigenic nature of HIV. Mass spectrometric characterization has provided further knowledge about the tertiary structure of the C5 region of HIV-gp120, and this information may be useful for vaccine development.
| Footnotes |
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2 Address correspondence and reprint requests to Dr. Kenneth B. Tomer, National Institute of Environmental Health Sciences, National Institutes of Health, P. O. Box 12233, Research Triangle Park, NC 27709. E-mail address: ![]()
3 Abbreviations used in this paper: MALDI, matrix-assisted laser desorption; TOF, time of flight; CNBr, cyanogen bromide. ![]()
Received for publication November 29, 1999. Accepted for publication February 10, 2000.
| References |
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1 peptide-binding domain. Eur. J. Immunol. 23:2016.[Medline]
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