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1 Lawrence Livermore National Laboratory, Macromolecular Crystallography, Biology and Biotechnology Research Program, University of California, Livermore, California 94551, USA
2 Army Medical Research Institute of Infectious Diseases, Laboratory of Molecular Immunology, Frederick, Maryland 21702, USA
3 Roche Bioscience, Palo Alto, California 94304, USA
Reprint requests to: Dr. Bernhard Rupp, Macromolecular Crystallography and Structural Genomics, Lawrence Livermore National Laboratory, LLNL-BBRP, POB 808, L-448, University of California; Livermore, CA 94551, USA; e-mail: br{at}llnl.gov; fax: (925) 424-3130.
(RECEIVED October 1, 2001; FINAL REVISION November 14, 2001; ACCEPTED November 26, 2001)
4 These authors contributed equally to this work. ![]()
Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.39702.
| Abstract |
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subunit of major histocompatibility complex class II (MHC-II) molecules. A comparison of hypothetical model complexes between SEA and the SEA triple mutant with MHC-II HLA-DR1 clearly shows disruption of key ionic and hydrophobic interactions necessary for forming the complex. Extensive dislocation of the disulfide loop in particular interferes with MHC-II
binding. The triple-mutant structure provides new insights into the loss of superantigenicity and toxicity of an engineered superantigen and provides a basis for further design of enterotoxin vaccines. Keywords: Enterotoxin; major histocompatibility complex; Staphylococcus aureus; vaccine design; X-ray structure
| Introduction |
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Staphylococcus bacteria infect their hosts opportunistically and cause pathology by expressing a number of protein toxins and other virulence factors. The protein toxins are responsible for a number of diseases, such as food poisoning, skin infections, bacterial arthritis, Kawasaki syndrome, rheumatic fever, and toxic shock syndrome (Scherer et al. 1993; Schlievert 1993).
The most well-characterized, structurally and immunologically, S. aureus toxins are the staphylococcal enterotoxins (SEs), which are single-chain proteins (2329 kD) subdivided into serotypes A, B, C1, C2, C3, D, E, G, and H (Marrack and Kappler 1990; Fleischer et al. 1995). SEs are superantigens and as such have the ability to stimulate whole T-cell subpopulations by cross-linking T-cell receptors (TCRs) with MHC-II molecules independent of the antigenic specificity of particular T-cells (Herman et al. 1991).
When acting as superantigens, SEs are not processed into smaller peptides for presentation by MHC-II but interact with MHC-II and TCR molecules as intact toxins (Scherer et al. 1993). Previous studies have revealed that TCRs are principally bound by SEs via hydrogen-bond interactions with the main-chain nitrogens and carbonyl oxygens of the ligand-recognition variable loops (CDR2 and HVR4) and via interactions with framework regions of the TCRß subunit variable domain (Vß; Choi et al. 1990; Fields et al. 1996).
SEs bind monovalently or bivalently to MHC-II molecules (Abramsen et al. 1995, Tiedemann et al. 1995). Some monovalent SEs (SEB, toxic shock syndrome toxin-1 [TSST-1]) bind exclusively to the conserved
-chain site (or low-affinity site), located outside the conventional peptide antigen-binding groove (Dellabona et al. 1990; Jardetzky et al. 1994; Kim et al. 1994), disrupting contacts between TCR and the MHC-bound peptide (Fields et al. 1996). Other monovalent superantigens (streptococcal pyrogenic exotoxin-C (SPE-C), for example) form contacts with the MHC-bound peptide and the polymorphic ß chain of MHC (Hudson et al. 1995; Abramsen et al. 1995) through a zinc-dependent site (or high-affinity site). Staphylococcal enterotoxin A (SEA), one of the most potent T-cell mitogens known, is a bivalent SE, as shown by mutagenesis and binding studies (Abramsen et al. 1995), interacting with MHC-II at both zinc-dependent and zinc-independent sites. The MHC-II
-binding region, located near the N terminus on SEA (912), is homologous to the MHC-II
binding site of SEB (Jardetzky et al. 1994); whereas, the C-terminal residues H187, H225, and D227 of SEA mediate zinc-dependent binding to H81 of the MHC-IIß through a tetrahedrally coordinating zinc (Abramsen et al. 1995; Hudson et al. 1995). Tiedemann et al. (1995) were able to isolate HLA-DR(SEA)2 hetero-trimers in solution and suggest SEA cross-links to two MHC-II molecules on the surface of antigen-presenting cells (Mehindate et al. 1995; Tiedemann et al. 1995, 1996). Kozono et al. (1995) proposed the formation of larger daisy-chain oligomers because the two binding sites do not appear to be competing. Studying the interaction of SEA mutants with either binding site disrupted (double-mutant H187A and H225A and triple-mutant F47S, L48S, and Y92A) with cell surface MHC-II, Tiedemann et al. (1996) concluded that both the high-affinity and low-affinity sites are required for superantigen function. They further proposed (MHC-II)2SEA formation is sufficient to induce cytokine production and may be sufficient to initiate a nonspecific T-cell response.
In contrast, the standard model of superantigen toxicity involves the formation of an MHC/TCR/superantigen complex, which circumvents the normal antigen-specific T-cell recognition (Dowd et al. 1995) but leads to nonspecific T-cell activation. SEs stimulate large fractions of whole T-cell populations (Kappler et al. 1992) by interaction with multiple subtypes of Vß subunits. The result is a polyclonal T-cell response of significantly greater magnitude than normal, antigen-specific, activation. Alhough (MHC-II)2SEA formation alone might be sufficient to cause cytokine production and T-cell stimulation, recent results (R.G. Ulrich, unpubl.) suggest that T-cell stimulation by SEA is likely to require engagement of the TCR by MHC-II-bound superantigen. By inducing massive T-cell proliferation, SEA causes the release of pathological levels of mast cell leukotrienes and proinflammatory cytokines, which is the basis of SEA's induced toxic shock syndrome (Stiles et al. 1993; Carlsson and Sjogren 1996).
Due to the growing threat from multi-drug-resistant S. aureus, efforts have been undertaken to create alternatives to antibiotic treatment for S. aureus-caused diseases. A highly promising approach is the development of vaccines against S. aureus infections based on the structure of superantigenic SE (Ulrich et al. 1998). SEA with mutations at the DR
-binding site can no longer form MHC-II/TCR/SEA or (MHC-II)2SEA complexes and therefore superantigen T-cell stimulation is prevented. Only conventional immune responses from processing and presenting of SEA-derived peptides to T-cells is then observed (Bavari et al. 1996). An engineered SEA triple mutant has been shown to trigger an efficient antibody response and has been shown to vaccinate mice and rhesus monkeys against SEA-triggered septicemia and death (Nilsson et al. 1999). In addition, antibodies produced against one SE vaccine cross-react with other SEs and superantigens by recognizing common structural epitopes. This cross-reactivity makes SE-based superantigen vaccines powerful tools in the fight against S. aureus infection and sepsis.
To explore the molecular basis of superantigen vaccine function, we have determined the structure of a nontoxic SEA triple mutant (L48R, D70R, and Y92A). Exploiting the common structural motifs between SEA and SEB MHC-II binding sites (Ulrich et al. 1995), homology models for both wild-type SEA and SEA triple-mutant complexes with MHC-II have been developed. These models provide key insights into altered behavior and loss of MHC-II
-chain binding and will provide for better rational vaccine design.
| Results |
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The final wFo
c Shake&wARP electron density map is continous for the whole polypeptide backbone for residues 6233 and very well defined for 96% of the amino acid residues. Residues 190 and 191 have poorly defined electron densities due to variable conformations. Side chains of surface exposed residues E9, K41, D60, K74, and E191 are only partly defined.
Structural comparison to wild-type SEA
The overall topology of the SEA triple mutant closely resembles that of the native protein (Schad et al. 1995), folding into two domains (domain I, residues 31116, and ß-barrel domain II, residues 117233). Domain II also includes the N-terminal segment 630. Introduction of three point mutationsL48R, D70R, and Y92A(Ulrich et al. 1995; Bavari et al. 1996) leads to formation of a bifurcated sheet sharing ß1 and ß4a strands in domain I (nomenclature derived from Schad et al. 1995).
The C
backbone of the mutant structure superimposes closely with wild-type SEA (rmsd of 0.53 Å for 199 C
, excluding residues 1147, 5159, 6492, 103200, and 208233), although mutations have caused notable alterations to some loops (Fig. 2
). Rmsd is 1.71 Å for all C
in common between the wild-type and mutant SEA. The most significant structure deviations occur in three regions known to be involved in formation of a complex with HLA-DR1
: between residue D45T51, residue Y91A105, and residue L198-L210. Residues 4551 are located between ß strands ß1 and ß2, forming a large reverse turn connecting the bifurcated sheets. The engineered R48 is situated at the outermost turn of this loop, causing its neighboring residues F47 and E49 to shift substantially from their native position (1.54 Å and 3.13 Å, respectively, on C
). R48 also forms a hydrogen bond (2.78 Å) with G98 backbone carbonyl in the adjacent loop.
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of C96 is moved 2.20 Å from its original position in the native structure, altering location and conformation of the disulfide bond. These movements and the formation of additional hydrogen bonds due to the point mutations L48R and D70R (H-bonds to G98O [2.78 Å] and Q95O [3.02 Å], respectively) are the likely cause of the loop region (91105) flip into a solvent exposed orientation (Fig. 2
Finally, major structural deviations occur in domain II, in region 198210, representing an expanded loop from L198 to Y205 and the five N-terminal residues of
-helix
5. Whereas Y94 and Q95 are entirely solvent exposed in native SEA, they are oriented toward the core of the molecule and more buried in the mutant. Relocation of this loop is mainly stabilized by hydrophobic interactions because the greatest effects are found around G203 and Y205, located at the loop turning points, which are shifted 4.66 Å and 3.08 Å, respectively, from their native C
positions (Fig. 2
). Crystal-packing interactions with symmetry-related molecules observed within proximity of the altered loop region 198210 are rather weak, partly due to their location at the end of the region, and are unlikely to significantly determine the conformation of this loop.
| Discussion |
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Homology models of ternary complexes
Similarity between SEA, SEB, and SPE-C and the availability of crystal structures of SEB and SPE-C complexes with MHC-II and TCR molecules (Jardetzky et al. 1994; Li et al. 1998; Li et al. 2001) make it possible to construct a hypothetical SEATCR(MHC-II)2 quaternary complex.
SEA and SEB are known to compete for binding to MHC-II molecules, indicating analogous binding mechanism and location at least at one binding site (Schad et al. 1995). Furthermore, SEA and SEB share 31% sequence homology (36% identity over 229 aligned C
atoms; rmsd 2.0 Å) and hence highly similar folds. ß-barrel and ß-grasp motifs (four-stranded mixed ß sheet with an
-helix packed across one face of the sheet; Overington 1992) are present in both structures. The C
alignment of wild-type SEA with the SEB (rmsd 2.0 Å) reveals differences primarily in the SEA N terminus, in loops of low-sequence homology, and in the disulfide-loop region (A90-V111; Ulrich et al. 1995). The recent publication of the SPE-C/MHC-II complex provides a basis for modeling the zinc-dependent interaction between SEA and MHC-IIß (Li et al. 2001). SEA and SPE-C bind the MHC-IIß chain similarly at the high-affinity binding site, contacting N-terminal residues of bound peptide.
The quaternary SEATCR(MHC-II)2 (Fig. 3
) is built by C
alignment of SEA in the modeled ternary complex with the SPE-C in the MHC-II
complex (Li et al. 2001). From the putative quaternary complex it appears the engineered mutations of the vaccine would have no effect on TCR binding and MHC-II binding at the zinc-dependent site. The binding regions that interact with MHC-II
at the zinc-independent site are significantly altered however.
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chain
complex
complex, most intermolecular interactions occur in three loop regions: residues 4450 (reverse turn), residues 90111 (disulfide-loop region), and residues 200212 (Fig. 4A
subunit. Additionally, SEB residues Y89 and Y115 form two hydrogen bonds with DR
-K39 (Fig. 4A
binding by 100-fold (Ulrich et al. 1995), emphasizing the key role of these anchoring residues. The SEB disulfide loop interacts with the
-helix from the DR1
domain through residues 9296, most significantly by Y94 (Jardetzky et al. 1994). The third loop region (200212) contacts the DR1 molecule at the C-terminal end of the DR1
-helix mainly through hydrogen bonds involving residues 210212 (Jardetzky et al. 1994).
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complex
site are conserved, as compared with SEBHLA-DR1
(Fig. 4B
are D45T51, Y91A105 (disulfide loop), and L198L210. Residues E67, Y89, and Y115 of the SEB-binding interface correspond to D70, Y92, and Y108 in SEA. Mutation of the SEA key residue Y92A resulted in 100-fold reduced HLA-DR1
; the single-site mutation Y108A has negligible effect on binding (Ulrich et al. 1995), although the homologous substitution in SEB (Y115A) has a substantial effect. The substitution of SEB E67 with the shorter carboxylate side chain of SEA D70 is thought to increase distances of Y92 and Y108 to DR
-K39 and therefore cause weaker interactions in the native SEAMHC-II complex. The weaker SEA Y108-DR
K39 interaction makes it easier to accommodate the Y108A substitution. Hydrogen bond formation between D70OD2 and
-K39NZ will require
-K39 to shift toward SEA to compensate for the shorter aspartate chain and optimize ion-pair interactions.
Engineered mutations disrupt binding
In vaccine design, SEA residues that primarily mediate HLA-DR
binding have been targeted to produce a vaccine devoid of pathological activity. The point mutations D70R and Y92A were engineered in the presented SEA triple mutant, accompanied by a mutation L48R added as a safety factor (Ulrich et al. 1998).
The D70R substitution leads to the disruption of the DR
-K39 salt bridge, one of the key interactions in DR
binding. Replacing the original aspartate by the bulkier and oppositely charged arginine causes both steric and charge repulsion (distance R70NH1
-K39NZ 1.23 Å). Further destabilization of interactions with HLA-DR
is achieved by the Y92A substitution. Due to the loss of a hydrogen bond acceptor and the large shift of residue 92 (10.3 Å) away from its position in the native structure, a potential hydrogen bond with DR
-K39 is eliminated. Only one intermolecular H-bond remains between the SEA triple mutant and HLA-DR1 (DR
/K39-SEA/Y108, 2.83 Å). This H-bond, if it forms, is insufficient to initiate or sustain binding with HLA-DR1. Furthermore, substitution D70R results in a new intramolecular hydrogen bond (R70NH1Q95O, 3.02 Å), stabilizing a conformation that disfavors HLA-DR1 binding.
L48 is found in the hydrophobic reverse turn and represents the only absolutely conserved residue in all bacterial superantigens (Ulrich et al. 1995) and L48 is essential for initial binding of MHC-II molecules. Inserting an arginine in this nonpolar loop introduces a particularly bulky and charged residue, leading to the disruption of the otherwise close fit of this loop into the predominantly hydrophobic groove on the DR
chain (Fig. 4C
). Interestingly, besides disrupting important interactions with the HLA-DR1
subunit, the two newly introduced arginines, R 48 and R 70, form an arginine cluster with R 211 and R 214 on the surface of the SEA mutant, preventing access of the MHC-II
chain by shielding the binding pocket and changing the surface polarity. The new hydrogen bonds formed by R 48 are also responsible for a cascade of structural rearrangements, affecting neighboring loop regions. The most striking result is the dislocation of disulfide-loop 91105 to solvent-exposed orientation (Fig. 4C
). The homology model positions the disulfide loop within such a short distance to the DR1 molecule that the loop virtually protrudes through the DR
-helix, suggesting binding of the SEA triple mutant will be substantially disfavored due to strong van der Waals repulsion forces.
Structural basis of vaccine efficacy
Binding assays showing the affinity of the SEA triple mutant for HLA-DR1 indicate a binding reduction of >102 compared to the wild-type protein (Fig. 1A
) and attenuated biological activity of >106 (Fig. 1B
). Discrepancies between apparent receptor-binding affinity and biological activity were noted previously (Leder et al. 1998). It is difficult to account for the substantial loss of binding by mutating the zinc-independent binding site alone, given that the zinc-dependent binding site is apparently unaffected by the engineered mutations. Reduced biological activity and altered SEA/MHC-II-binding stoichiometry would be expected, along with intact zinc-dependent binding. A full explanation of these findings requires further investigation and some zinc-mediated binding to HLA-DR1 cannot be ruled out. Possible binding to the zinc-dependent site in the absence of zinc-dependent site interactions has been shown by Tiedemann et al. (1995). A different triple mutantF47S, L48S, and Y92Apredicted to exhibit defective interaction with DR
, showed residual binding to cell-surface MHC-II (Tiedemann et al. 1995). Bivalent receptor-binding surfaces of SEA promote cross-linking of MHC-II molecules on the cell surface, increasing biological potency (Tiedemann et al. 1995). Loss of DR
binding is likely to prevent TCR binding in an orientation that is favorable to T-cell stimulation (Ulrich et al. 1995). In the X-ray structure, Zn2+ is tetrahedrally complexed by H187, H225, and D227 and H44 of a symmetry-related SEA triple-mutant molecule. H44 is located within the engineered N-terminal-loop region harboring L48R of the SEA mutant. This suggests a possible dimerization of the SEA triple mutant in a head-to-tail arrangement that would block binding at the high-affinity site. Therefore reduced MHC-II binding could be explained even though the zinc-binding site is not directly affected by the engineered mutations. However, the available evidence suggests that the SEA triple mutant is predominately monomeric in solution (Ulrich, unpubl.).
The crystal structure of SEA vaccine provides the structural basis for understanding the loss of superantigenicity in the SEA triple mutant. Consistent with biochemical and cellular assays, the SEA vaccine X-ray structure and the homology model show that the combination of the three mutations L48R, D70R, and Y92A severely disrupts zinc-independent binding of SEA to MHC-II. Without DR
binding, the productive formation of ternary or quaternary complexes is impaired and superantigenic stimulation of T-cells is prevented.
Engineering of a defective zinc-binding site could contribute to further vaccine development, given that SEA-mediated cross-linking requires this site and stimulates T-cell independent release of cytokines, a response also mimicked by antibody-mediated MHC-II cross-linking (Mehindate et al. 1995). However, Fig. 1B
shows that disrupting the low-affinity, zinc-independent binding site is sufficient to abolish superantigenicity in SEA. Overall, structural and biomedical data confirm the utility and efficacy of the SEA triple mutant as a potent immunogen and as a safe vaccine. This vaccine may provide immunity to multiple bacterial superantigens because antibodies produced against SEA display cross-reactivity against other SEs. The SEA triple mutant may serve as a model for structure-based rational design of other SE and superantigen vaccines. Facing the increasing threat of multi-antibiotic-resistant Staphylococcus strains, a potential superantigen vaccine provides important contributions in the fight against a number of S. aureus-triggered human diseases.
| Materials and methods |
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Human T-cell recognition of SEA
Human peripheral blood mononuclear cells were purified by Ficoll-hypaque (Sigma) buoyant density gradient centrifugation and cultured with wild-type or mutant SEA in RPMI-1640 with 5% fetal bovine serum. Following 72 h of culture, the mononuclear cells were pulse-labeled for 12 h with 1µCi [3H]-thymidine (Amersham) and harvested onto glass-fiber filters. Incorporation of [3H]-thymidine into the cellular DNA was measured by liquid scintillation (TopCount; Wallac Inc.).
Protein crystallization, data collection, and processing
The SEA triple mutant was expressed and purified as described previously (Ulrich et al. 1995; Bavari et al. 1996). Crystals were obtained at 4°C by hanging drop vapor diffusion (McPherson 1982) in 8 µL drops (4 µL of the reservoir solution, 10% PEG 6000, 5% MPD, and 0.1 M HEPES at pH 7.8 and 4 µL protein stock solution of 2 mg/mL) suspended over a 1-mL reservoir. X-ray diffraction data were collected with a Quantum4 ADSC CCD detector from a single cryo-cooled crystal (Oxford Cryosystems) on Advanced Light Source (ALS) beamline 5.0.2 at
= 1.1000 Å. A total of 130 images were collected with an oscillation range of 1°. Crystals were diffracted to 1.5 Å. The crystal belonged to space group P212121 with the unit cell parameters a = 39.05, b = 78.65, and c = 86.37 Å. Calculation of Vm (Matthews 1968) indicated one molecule in the asymmetric unit (Vm = 2.62 Å3/Da) and an approximate solvent content of 52%. The data were indexed and integrated with MOSFLM (CCP4 1994) and scaled with SCALA and TRUNCATE from the CCP4 program suite (CCP4 1994).
Structure determination and refinement
The structure was solved by molecular replacement using EPMR (Kissinger et al. 1999) with native SEA (1ESF; Schad et al. 1995) as a search model (minus cadmium ion). Initial maps were generated with Shake&wARP (Segelke et al. 2000), a modified version of wARP (Perrakis et al. 1997), in combination with REFMAC unrestrained maximum-likelihood minimization (Murshudov et al. 1997). Model building was performed with XtalView (McRee 1992) using the wild-type SEA structure as a template. Solvent structure was built by manual placement and by iteratively using ARP (Lamzin and Wilson 1993) and REFMAC (Murshudov et al. 1997). Further refinement was carried out with REFMAC and Xplor (Brünger 1992a) and included bulk solvent correction, overall anisotropic B-factors, rigid body refinement, prepstage, group B-factor, and final individual B-factor refinement.
Structural analysis and homology models
Sequence alignments were performed with BLAST search (Altschul et al. 1997); structure alignments were performed with the DALI server (Holm and Sander 1996). Homology models were developed using X-ray coordinate data from the following PDB files: 1ESF, 1SEB, 1SBB, 1HQR, and 1AO7 (Jardetzky et al. 1994; Schad et al. 1995; Garboczi et al. 1996; Li et al. 1998, 2001). Superposition of molecules and rmsd calculation were done with the program Midas (Ferrin et al. 1988).
Figures
Secondary structure assigned according to Kabsch and Sander (1983). Figures were drawn with MOLSCRIPT (Kraulis 1991) version 2.1.2 using the POVSCRIPT patch (copyright Dan Peisach) and rendered with POV-Ray (Persistance of Vision Raytracer, v.3.1g, 1999).
| Acknowledgments |
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The publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 USC section 1734 solely to indicate this fact.
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