Protein expression and purification

The design of a construct amenable to high-level expression of Zaire ebolavirus GP_1,2 (ZEBOV-GP_1,2) and KZ52 is described previously [17], [18]. Briefly, ZEBOV-GP_1,2 has an N-terminal HA tag and comprises residues 33–632 with the mucin and transmembrane regions (residues 313–465 and 633–676) deleted, and a T230V mutation that significantly improves expression yields. The protein was transiently expressed in HEK293T cells and purified using an anti-HA column followed by size exclusion chromatography. ZEBOV-GP_1,2 is cleaved by thermolysin (75 µg/ml) overnight and the cleaved protein (ZEBOV-GP_1,2CL) is separated from released fragments by size exclusion chromatography using a Superdex-200 10/300 GL column equilibrated in PBS buffer. To obtain a complex between ZEBOV-GP_1,2CL and KZ52, the proteins were mixed in a ratio of 1∶1.5 by weight respectively and incubated on ice for 2 h. The complex was separated from excess KZ52 by size exclusion chromatography (Suppl. Figure S1A).

A construct for Sudan ebolavirus GP_1,2 (SEBOV-GP_1,2; strain Gulu) was cloned into the pDISPLAY vector and contains a N-terminal HA tag for purification. The construct comprises residues 33–637 with the mucin and transmembrane regions (residues 314–472 and 638–676) deleted. SEBOV-GP_1,2 is more sensitive to cathepsin and thermolysin cleavage and it is difficult to obtain sufficient yields of cleaved, wild-type SEBOV-GP_1,2 for DXMS studies. Hence, for production of homogeneous SEBOV-GP_1,2CL, a furin cleavage site was introduced with the mutation ²⁰⁵RKKR²⁰⁸ into the 190–213 loop upon which cathepsins and thermolysin act (gift of Paul Bates, University of Pennsylvania). This protein is thus “born” cleaved twice by furin in the producer cell: one furin-cleavage site separates GP1 from GP2, while the second removes the glycan cap from GP1. This “born-cleaved” protein was transiently expressed in HEK293T cells supplemented with a plasmid encoding excess furin (in a glycoprotein-to-furin plasmid ratio of 4∶1 by weight). The expressed protein was purified using an anti-HA column. Further size exclusion chromatography illustrates it is the same size as cleaved wild-type GP_1,2.

Effect of pH on KZ52 binding to GP_1,2CL

Binding of KZ52 to ZEBOV-GP_1,2CL under various pH conditions was determined by ELISA. Briefly, aliquots of ZEBOV-GP_1,2CL were buffer exchanged to a range of pH (pH 4.2, 4.6, 5.0, 5.4, 6.0, 6.6 and 7.0, each obtained from a 1 M stock solution pH screen (Hampton) using Millipore Ultramax 10 K cutoff centrifugal concentrators [17]), and incubated in 10 mM buffer and 150 mM NaCl at room temperature for 2 h. The proteins were subsequently neutralized in 100 mM Tris-HCl buffer pH 7.5 (note that any conformational changes in GP2 leading to fusion are irreversible). The changes in pH were monitored by litmus paper.

0.25 µg of the protein per well was adsorbed (∼50 µl/well) overnight at 4°C in a 96-well microtiter plate. The wells were washed with PBS containing 0.05% Tween (PBS-Tween) and blocked with 100 µl/well of 3% bovine serum albumin (BSA) in PBS for 1 h at room temperature. The wells were washed (with PBS-Tween) and incubated with 50 µl of the antibody between 0.1 and 1 µg/ml for 1 h, washed again, and incubated with HRP conjugate (1∶2000 dilution in 1% BSA and PBS). The wells were washed thoroughly with PBS-Tween, and bound HRP was detected by incubation with 50 µl/well of 1∶1 solution of TMB substrate (Pierce). The reaction was terminated by addition of 50 µl/well of 2 N H₂SO₄. The resulting solutions were analyzed by a UV/Vis spectrophotometer microtiter plate reader at 450 nm.

DXMS methodology - Optimization of fragmentation conditions

Prior to the exchange experiments, disulfide reduction and protein denaturation conditions were identified that produced an optimal pepsin fragmentation pattern under exchange-quench conditions. It was found that incubation with quench buffer with TCEP and denaturant, followed by dilution of denaturant prior to exposure to pepsin gave the best peptide probe coverage map. For ZEBOV, 1 µl of ZEBOV-GP_1,2 or ZEBOV-GP_1,2CL stock solution (at 5.3 mg/ml and 5.5 mg/ml respectively) was diluted into 1 µl of non-deuterated buffer (8.3 mM Tris, pH 7.5, 150 mM NaCl, in H₂O) at 0°C. Next, 3 µl of 1 M TCEP, 6.4 M GuHCl, pH 2.85 (quench buffer) was added and the sample was incubated for 5 min on ice. Then 15 µl of 0.8% formic acid (FA), 16.6% glycerol (quench diluent) was added to the denatured sample prior to protease digestion.

For SEBOV, 1 µl of SEBOV-GP_1,2 stock solution (6.3 mg/ml) was diluted with 7 µl of non-deuterated buffer (8.3 mM Tris, 150 mM NaCl, in H₂O, pH 7.15) at 0°C and then quenched with 12 µl of quench buffer containing 3.2 M GuHCl, 15 mM TCEP, 0.8% formic acid, 16.6% glycerol (pH 2.4). For SEBOV-GP_1,2CL sample, 2 µl of protein (5.1 mg/ml) stock solution was diluted into 3 µl of quench buffer (1 M TCEP, 6.4 M GuHCl, pH 2.85) and the sample was incubated for 5 min on ice. Then 15 µl of quench diluent (0.8% FA, 16.6% glycerol) was added. The samples were then frozen on dry ice and stored at −80°C for further analysis.

In order to demonstrate the ability of our methods to detect differences in deuteration of these proteins, GP1 and GP2 of SEBOV-GP1,2_CL were separated from each other by adding 10 mM DTT and heating at 37°C for 30 min. The disulfide-reduced sample was prepared and analyzed in a similar fashion as SEBOV-GP1,2_CL for DXMS experiments (Figures S4A–S4C in supplementary information).

All samples were subsequently thawed at 4°C and passed over an AL-20-pepsin column (16 µl bed volume, 30 mg/ml porcine pepsin (Sigma)), at a flow rate of 20 µl/min. The resulting peptides were collected on a C18 trap (Michrom MAGIC C18AQ 0.2×2) and separated using a C18 reversed phase column (Michrom MAGIC C18AQ 0.2×50 3 µm 200 Å) running a linear gradient of 0.046% (v/v) trifluoroacetic acid, 6.4% (v/v) acetonitrile to 0.03% (v/v) trifluoroacetic acid, 38.4% (v/v) acetonitrile over 30 min with column effluent directed into an LCQ mass spectrometer (Thermo-Finnigan LCQ Classic). Data were acquired in both data-dependent MS1∶MS2 mode and MS1 profile mode. SEQUEST software (Thermo Finnigan Inc.) was used to identify the sequence of the peptide ions. DXMS Explorer (Sierra Analytics Inc., Modesto, CA) was used for the analysis of the mass spectra as described previously [19].

Deuterium exchange experiments

Functional deuteration of ZEBOV glycoproteins were performed by diluting 1 µl of ZEBOV-GP_1,2CL or ZEBOV-GP_1,2 stock solution into 3 µl of D₂O buffer (8.3 mM Tris, 150 mM NaCl, in D₂O, pD_READ 7.2) at 0°C. At 10 sec and 1000 sec, 6 µl of ice-cold quench buffer (6.4 M GuHCl, 1 M TCEP, pH 2.85) was added, samples incubated on ice for 5 min, 10 µl quench diluent (0.8% FA, 16.6% glycerol) was added, and samples frozen on dry ice. The equilibrium-deuterated back-exchange control samples were prepared by diluting 1 µl of ZEBOV-GP_1,2CL or ZEBOV-GP_1,2 into 3 µl of 1% formic acid in 99.9% D₂O with incubation overnight at room temperature, cooled to 0°C and mixed with 6 µl quench buffer, incubated for 5 min, supplemented with 10 µl quench diluent, and frozen and further processed as above.

Functional deuteration of SEBOV-GP_1,2 was performed by first diluting 2 µl of SEBOV-GP_1,2 with 2 µl of non-deuterated buffer (8.3 mM Tris, 150 mM NaCl, in H₂O, pH 7.15). At 0°C, 4 µl of D₂O buffer (8.3 mM Tris, 150 mM NaCl, in D₂O, pD_READ 7.2) was added. At 10 sec and 1000 sec, 12 µl of ice-cold quench buffer (3.2 M GuHCl, 15 mM TCEP, 0.8% formic acid, 16.6% glycerol, pH 2.4) was added. For the SEBOV-GP1,2_CL sample, 2 µl of SEBOV-GP_CL (5.95 mg/ml) stock solution was diluted into 2 µl of D₂O buffer (8.3 mM Tris, 150 mM NaCl, in D₂O, pD_READ 7.2) at 0°C. At 10 sec and 1000 sec, 6 µl of ice-cold quench buffer (6.4 M GuHCl, 1 M TCEP, pH 2.85) was added, samples incubated on ice for 5 min, 15 µl quench diluent (0.8% FA, 16.6% glycerol) was added.

The centroids of the isotopic envelopes of nondeuterated, functionally deuterated, and fully deuterated peptides were measured using DXMS Explorer and then converted to corresponding deuteration levels with corrections for back-exchange [20].

Figure preparation

All figures in the manuscript were generated using Pymol and Adobe photoshop.

Structure and Neutralizing antibodies of ZEBOV and SEBOV

The crystal structure of Zaire ebolavirus GP_1,2 (ZEBOV-GP_1,2) has been previously determined in its prefusion form, in complex with an antibody termed KZ52 that was derived from a human survivor of Zaire ebolavirus infection [17]. The structure reveals that antibody KZ52 binds a conformational epitope on GP_1,2 where the GP1 and GP2 subunits meet, and illustrates the specificity of KZ52 for the prefusion state of ZEBOV-GP_1,2. In addition, we have also determined the crystal structure of the prefusion form of Sudan ebolavirus GP_1,2 (SEBOV-GP_1,2) bound to a novel neutralizing antibody termed 16F6 [21]. 16F6, like KZ52, recognizes a conformational epitope on the prefusion form of SEBOV-GP_1,2 that bridges the two subunits together. The loop of GP_1,2 upon which both endosomal cathepsins and thermolysin act (residues 190–213) is mobile and disordered in both structures, and is located at the outer (“side”) surface of the trimeric GP_1,2.

In these prefusion GP_1,2 structures, each GP2 in the trimer wraps around its corresponding GP1 in a metastable state. The GP1s form a “clamp” on the metastable prefusion conformation of GP2 and prevent it from springing irreversibly into its fusion-active and more stable six-helix bundle conformation, which has also been crystallized [22], [23]. In order for fusion to occur, GP2 must unwrap from each GP1 in the prefusion complex and rearrange to yield the six-helix bundle conformation of GP2 alone.

Priming GP_1,2

To investigate the effects of enzymatic cleavage of GP_1,2, we digested ZEBOV-GP_1,2 with thermolysin and purified the resulting protein (ZEBOV-GP_1,2CL) by size exclusion chromatography. Note that the ZEBOV-GP_1,2 used for the studies has a deletion of the mucin-like domain to enhance protein expression. Thermolysin functionally mimics cleavage by endosomal cathepsins, but operates at physiological pH, while cathepsins require low pH (∼5.5) for cleavage. Use of thermolysin allows us to decouple the effects of enzymatic cleavage from the effects of low pH. The elution profile of thermolysin-cleaved ZEBOV-GP_1,2CL suggests that ZEBOV-GP_1,2 remains trimeric after cleavage (Suppl. Figure S1A).

SEBOV-GP_1,2 is quite sensitive to proteolysis and cleavage by either cathepsins L/B or thermolysin results in significant degradation, making it difficult to purify sufficient material for DXMS studies. In order to analyze the effects of enzymatic cleavage of SEBOV-GP_1,2, we engineered a version of SEBOV-GP_1,2 with an additional furin site at residues 206–210 in the loop of GP1 that is operated on by cathepsins and thermolysin (the wild-type furin-cleavage site that separates GP1 and GP2 also remains in this construct). The furin-engineered SEBOV-GP_1,2CL, is stable, is released from the expression host already deleted of its glycan cap and mucin-like domain and structurally mimics enzymatically cleaved SEBOV-GP_1,2 (Suppl. Figure S1B). Like ZEBOV-GP_1,2CL, SEBOV-GP_1,2CL also exists as a trimer.

Analysis of conformational changes by DXMS

DXMS is able to measure the ability of deuterium in solvent water to exchange with hydrogens that are covalently bound to peptide amide nitrogen atoms in a protein [24]. To determine if cleavage of GP_1,2 results in conformational change, we analyzed uncleaved ZEBOV/SEBOV-GP_1,2 and cleaved ZEBOV/SEBOV-GP_1,2CL proteins by DXMS, obtaining 49%/68% and 68%/83% coverage, respectively. Peptide regions throughout the glycoproteins were analyzed. Peptides covalently linked to glycans of heterogeneous mass are not accessible for measurement with currently employed DXMS methods, and therefore result in small gaps in the sequence coverage. Note that enzymatic cleavage removes nearly all N-linked glycans from GP1 and hence greater sequence coverage is obtained for cleaved GP (68%/83%) than uncleaved GP (49%/68%).

For ZEBOV-GP_1,2 the peptide fragmentation analysis confirms that thermolysin cleaves after the aromatic residues in the disordered loop ¹⁹⁰KKDFFSS¹⁹⁶ and deletes the glycan cap (as observed by Dube et. al. [15]). The deuteration levels of ZEBOV-GP_1,2 and SEBOV-GP_1,2 (measured over a time of 10–1000 sec) are consistent with the respective crystal structures (PDB code 3CSY and 3S88) in that peptide fragments that are buried or that have amide hydrogen atoms involved in hydrogen bonding show low levels of deuteration.

Comparison of uncleaved GP_1,2 with cleaved GP_1,2CL, for both ZEBOV and SEBOV, reveals that no significant changes in deuteration occur upon cleavage for any measured peptide spanning the whole of GP_1,2, observed over a 10–1000 sec time scale (Figure 1 and S2A–S3C in supplementary information). The deuteration pattern of the residues in the fusion loop (residues 520–540 of GP2) is also identical between the cleaved and uncleaved proteins (Figure 2). The unwinding of the fusion loop is a required early step in the springing of GP_1,2CL to the post-fusion form. Alteration in the deuteration pattern of the fusion loop could indicate the beginning of unwinding of GP1,2_CL, but is not observed after enzymatic cleavage.

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Figure 1. Representative deuteration of peptide fragments of ZEBOV-GP_1,2.

Plots of deuteration of peptides of ZEBOV-GP_1,2 (shown in dark blue) and ZEBOV-GP_1,2CL (shown in magenta) over a time period of 10–1000 sec. Representative peptides are taken from residues adjacent to the glycan cap of GP1 (Panel A: residues 82–94), the base subdomain core region of GP1 (Panel B: residues 166–176), a partially exposed region N-terminal of the trimeric interface of GP2 (Panel C: residues 572–581) and the trimeric interface of GP2 (Panel D: residues 582–593). Deuteration plots of the detected peptides of entire cleaved and uncleaved GP_1,2 are illustrated in Suppl. Figures S2A–S3C.

https://doi.org/10.1371/journal.pntd.0001395.g001

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Figure 2. The fusion loop of ZEBOV-GP_1,2.

(A) Cartoon representation of the fusion loop of GP2 (shown in ball-and-stick representation with carbon atoms colored orange). GP1 subunits of the 3-fold related protomers are shown in different shades of blue. One of the GP2 subunits is shown in orange, and the other two are shown in grey. The crystallographically disordered loop that is cleaved by cathepsin L/B is shown as a dotted line. (B) Deuteration plots of the residues in the fusion loop in ZEBOV-GP_1,2 (shown in dark blue) and ZEBOV-GP_1,2CL (shown in magenta).

https://doi.org/10.1371/journal.pntd.0001395.g002

In ZEBOV, residues R64, F88, K95, K114, K115, and K140 are critical for binding and are thought to comprise a part of the receptor-binding region [15], [25]. Peptides containing the residues R64, F88, K95, K114, and K115 are equally accessible by solvent before and after cleavage and removal of the glycan cap (Figure 3), indicating that no major conformational changes occur at these sites upon cleavage. Note that peptides containing residue K140 are not detected in DXMS of ZEBOV/SEBOV GP_1,2 or GP_1,2CL, and so it is not possible to compare deuteration levels of K140. Of this set of residues, F88, K114, K115 and K140 are inward of the glycan cap and solvent-accessible, and could potentially interact with the receptor. Residues R64 (K64 in SEBOV) and K95 are buried and probably have auxillary roles in receptor binding. Alternately, a conformational change could occur upon receptor binding that brings R64 and K95 into direct contact with the receptor.

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Figure 3. Residues important for attachment.

Ribbon representation of a model of the cleaved ZEBOV-GP_1,2CL trimer with residues R64, F88, K95, K114, K115 and K140, which have been identified by mutagenesis as important for attachment, shown in ball-and-stick with carbon atoms colored yellow. GP1 subunits are shown in different shades of blue and the GP2 subunits are shown in different shades of grey. Peptides containing residues R64, F88, K95, K114 and K115 do not undergo measurable conformational change upon priming of ZEBOV-GP_1,2.

https://doi.org/10.1371/journal.pntd.0001395.g003

DXMS thus suggests that no residues in ZEBOV/SEBOV-GP_1,2CL dramatically change conformation when the mucin-like domain and glycan cap are released. These results also suggest that the glycan cap, itself, does not significantly occlude access by solvent to this site. The glycan cap, however, could block steric access by a protein molecule and receptor access would likely be enhanced by enzymatic removal of the glycan cap.

The epitope of the human neutralizing antibody KZ52 bridges GP1 and GP2 and KZ52 only binds when the subunits are assembled in their prefusion conformation. Conformational changes in GP2, such as those required for fusion, would likely abrogate KZ52 binding. Hence, binding studies of KZ52 to ZEBOV-GP_1,2CL provide additional insights into the structure of ZEBOV- GP_1,2CL. By both size exclusion chromatography and ELISA, we find that KZ52 binds well to cleaved, trimeric ZEBOV-GP_1,2CL (See Figure 4 and Suppl. Figure S1A). An equivalent, GP1/GP2-bridging, prefusion-specific antibody, termed 16F6 [21], that recognizes SEBOV-GP_1,2 also forms a stable complex with SEBOV-GP_1,2CL. The binding of the prefusion-specific conformational antibodies KZ52 and 16F6 indicates that the GP_1,2CL ectodomain from both viruses remains in its pre-fusion state upon thermolysin or furin cleavage of the 190–213 loop. In addition, successful binding of KZ52 to cathepsin L-cleaved ZEBOV-GP_1,2CL with a K_D of 1.5 nM has been recently reported by Hood et al. using surface plasmon resonance [16]. By contrast, Shedlock et al. [26] find that KZ52 does not neutralize cathepsin L-cleaved ZEBOV-GP_1,2 that has been pseudotyped onto a viral surface (binding not directly measured in these studies). Hence, it seems that some as-yet-undetermined differences exist between ectodomain GP and viral-surface GP upon cathepsin L cleavage that do not occur upon thermolysin cleavage.

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Figure 4. Binding of KZ52 to ZEBOV-GP_1,2CL incubated at endosomal pH.

Plot of KZ52 binding at 1.0, 0.33, and 0.11 µg/ml (blue, light blue and grey, respectively) to ZEBOV-GP_1,2CL in ELISA. Bovine serum albumin (BSA) and denatured ZEBOV-GP1,2_CL (Denat.) were used as negative controls. Control ZEBOV-GP_1,2CL was maintained at pH 7.5.

https://doi.org/10.1371/journal.pntd.0001395.g004

Effect of pH on conformation of primed GP_1,2

The endosomal compartments have an acidic pH ranging from ∼5.9–6.0 in the early endosome to ∼5.0–5.5 in the late endosome and the role of this low pH in triggering irreversible conformational changes leading to fusion has been speculated. To investigate the effect of pH on the conformation of ZEBOV-GP_1,2CL, we monitored binding of KZ52 to acid pH-treated ZEBOV-GP_1,2CL by ELISA (Figure 4). Bovine serum albumin (BSA), and reduced and denatured GP_1,2 were used as negative controls. Indeed, KZ52 binding is unaffected by incubation of ZEBOV-GP_1,2CL in endosomal pH, suggesting that pH alone does not cause rearrangement of ZEBOV-GP_1,2CL from the pre-fusion state.

Conclusions

The DXMS and ELISA binding studies together suggest that the priming of GP_1,2 of ebolaviruses and the low pH in which priming occurs, are themselves, insufficient for triggering the conformational changes required for fusion. An additional trigger such as binding of the receptor to cleaved GP or the action of another cellular factor thus appear to be essential for fusion (Figure 5).

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Figure 5. Changing structures of ZEBOV-GP_1,2.

Cartoon representations of GP_1,2 in its viral surface form (PDB: 3CSY), putative receptor-binding form and post-fusion form (PDB: 2EBO). GP1s and GP2s are colored in different shades of blue and grey, respectively. The mucin-like domains were deleted from ZEBOV-GP_1,2 for crystallization and have been modeled here as not-to-scale balloons. It is currently unclear if GP1 remains attached to GP2 during the conformational changes that lead to fusion. The transmembrane regions at the bottom of GP_1,2 are not illustrated.

https://doi.org/10.1371/journal.pntd.0001395.g005

The requirement of enzymatic cleavage for ebolavirus GPs may instead serve different, non-exclusive purposes. Cleavage might simply expose the receptor-binding site for binding to an endosomal receptor. Further, removal of the glycan cap and the heavily glycosylated mucin domain (∼75 kDa of protein and carbohydrate) could facilitate membrane fusion by reducing steric barriers to GP2 rearrangement and membrane association. Alternatively, cleavage of the residue 190–213 loop that covers the outside of the fusion loop may remove a flexible tether that anchors the fusion loop in place on the outside of the prefusion trimer. The enzymatic cleavage step of ebolavirus GP_1,2 could indeed be required for one or all of these reasons, but the specific trigger of ebolavirus fusion remains to be identified.