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Proc Natl Acad Sci U S A. Jul 8, 2008; 105(27): 9175–9180.
Published online Jul 2, 2008. doi:  10.1073/pnas.0803275105
PMCID: PMC2453692
Biochemistry

Atomic resolution structural characterization of recognition of histo-blood group antigens by Norwalk virus

Abstract

Members of Norovirus, a genus in the family Caliciviridae, are causative agents of epidemic diarrhea in humans. Susceptibility to several noroviruses is linked to human histo-blood type, and its determinant histo-blood group antigens (HBGAs) are regarded as receptors for these viruses. Specificity for these carbohydrates is strain-dependent. Norwalk virus (NV) is the prototype genogroup I norovirus that specifically recognizes A- and H-type HBGA, in contrast to genogroup II noroviruses that exhibit a more diverse HBGA binding pattern. To understand the structural basis for how HBGAs interact with the NV capsid protein, and how the specificity is achieved, we carried out x-ray crystallographic analysis of the capsid protein domain by itself and in complex with A- and H-type HBGA at a resolution of ≈1.4 Å. Despite differences in their carbohydrate sequence and linkage, both HBGAs bind to the same surface-exposed site in the capsid protein and project outward from the capsid surface, substantiating their possible role in initiating cell attachment. Precisely juxtaposed polar side chains that engage the sugar hydroxyls in a cooperative hydrogen bonding and a His/Trp pair involved in a cation–π interaction contribute to selective and specific recognition of A- and H-type HBGAs. This unique binding epitope, confirmed by mutational analysis, is highly conserved, but only in the genogroup I noroviruses, suggesting that a mechanism by which noroviruses infect broader human populations is by evolving different sites with altered HBGA specificities.

Keywords: norovirus, receptors, x-ray crystallography, cation–π interaction

Noroviruses (NoVs), which constitute one of the four genera in the family Caliciviridae, are nonenveloped, icosahedral viruses with a positive-sense single-stranded RNA genome (1). These highly contagious human pathogens are the major cause of acute epidemic nonbacterial gastroenteritis worldwide and account for an estimated ≈23 million cases each year in the United States alone (2). Based on phylogenetic analysis, the Norovirus genus is classified predominantly into two genogroups (GI and GII), each of which consists of several genotypes, and minor genogroups that include the murine and bovine noroviruses (35). The norovirus genome consists of three open reading frames (ORFs). ORF1 encodes the nonstructural proteins that are essential for virus replication, whereas ORF2 and ORF3 encode a major capsid protein VP1 and a minor structural protein VP2, respectively. VP1 self-assembles into virus-like particles (VLPs) that are morphologically and antigenically similar to native virions (6, 7). Because NoVs are noncultivatable in cell culture, much of our understanding of the biology of human NoVs has come from studies using VLPs.

The x-ray crystallographic structure of the recombinant Norwalk virus (NV) capsid (≈390 Å in diameter), determined to 3.4-Å resolution, shows that the capsid exhibits a T=3 icosahedral organization formed by 90 dimers of the capsid protein (8) (Fig. 1a). The NV capsid protein VP1 has two distinct domains, the shell (S) domain formed by amino acid residues 1–225 and the protruding (P) domain formed by residues 225–530 (Fig. 1b). The S domain is involved in the formation of the icosahedral shell, whereas the P domain is involved extensively in the dimeric contacts (Fig. 1 a and b). The dimers of the P domain project out from the icosahedral shell at the local and the strict twofold axes and surround the large hollows (or depressions) at the icosahedral fivefold and threefold axes of the T=3 lattice. Based on the location of the P domain in the capsid structure and sequence comparison with other NoVs, it was hypothesized that the P domain would be involved in immunogenicity, strain diversity, and receptor binding. This was substantiated by subsequent studies with monoclonal antibodies, synthetic carbohydrates, and mutational analysis on both GI and GII noroviruses (912).

Fig. 1.
P domain dimer has the same conformation as in the whole capsid structure. (a) The T=3 capsid structure (showing only the backbone atoms) of NV, determined to 3.4-Å resolution (8), formed by 90 dimers of the capsid protein VP1. Shown are the S ...

Several observations suggest that histo-blood group antigens (HBGAs), which are genetically determined glycoconjugates found in mucosal secretions and on epithelial cells, including intestinal epithelial cells (13), function as receptors for NoVs (10, 1416). Volunteer studies have shown that susceptibility to NoV infection depends on a person's HBGA expression. Binding studies using NoV VLPs with saliva, red blood cells, and synthetic carbohydrates demonstrate direct interaction between VLPs and HBGAs. Importantly, VLPs from NV, the prototype GI NoV, attach to the surface of epithelial cells at the gastroduodenal junction of donors with secretor positive status, further substantiating the involvement of HBGAs in cell attachment of NoVs (10). These and other studies have indicated that specificity for HBGA is strain-dependent across the two genogroups (1720). The majority of GI NoVs interact with H- and A-type HBGAs and Lewis antigens Leb and Ley (11), whereas GII NoVs exhibit more diverse HBGA binding patterns including the B-type HBGA (12, 20, 21) [see supporting information (SI) Fig. S1 for definitions of HBGAs]. The structural basis for these strain-dependent NoV interactions with HBGAs is not clear. We undertook crystallographic studies of the NV capsid protein to address questions such as how noroviruses recognize specific HBGAs, despite their differences in carbohydrate composition; whether these HBGAs share a common binding site; and whether the location and orientation of the bound HBGAs support their proposed role in cell attachment.

Results and Discussion

To enable higher-resolution structural analysis of the HBGA binding characteristics, we carried out structural studies using only the P domain instead of the entire capsid. The P domain (amino acids 225–519) was expressed in Escherichia coli and purified by using a series of column chromatographic steps. Chromatographic analysis showed that the purified P domain formed dimers consistent with previous observations (22). The P domain was first crystallized alone and then in complexes with penta- and trisaccharides corresponding to the terminal carbohydrates of H-type 1 and A-type HBGAs (Fig. S1), respectively. All of the crystals exhibited the same space group symmetry with two molecules of the P domain in the crystallographic asymmetric unit, and diffracted to a similar resolution of ≈1.4 Å (Table S1). The crystallographic structures of the P domain alone, and bound to H- and A-type HBGA, were determined by molecular replacement (MR) techniques with the P domain from the previously determined NV capsid structure (PDB entry 1IHM) as the search model.

Unliganded P Domain Structure.

Consistent with the chromatographic analysis, the two P domain molecules in the crystallographic asymmetric unit interact extensively to form a dimer. With the exception of high-resolution details, including well defined side-chain orientations and solvent molecules, the structure of the P domain dimer is similar to that seen in the whole capsid structure with a root mean squared deviation (RMSD) of 0.8 Å, thus validating the use of the P domain alone in the ligand binding studies (Fig. 1). In the capsid structure, the quasi-equivalent A–C subunits form A/B and C/C dimers (8). Except for the relative orientations between the P and S domains, modulated by an intervening hinge region (amino acids 225–229), the P domain structures are identical in these quasi-equivalent dimers. In the present structure also, the two subunits of the dimer, although not related by the crystallographic symmetry, are identical with a RMSD of 0.3 Å. As in the capsid structure, amino acid residues 225–278 and 406–519 form the P1 subdomain, and residues 279–405 form the distal P2 subdomain, which exhibits the most amino acid sequence variability among caliciviruses.

The P domain is comprised of several β-strands and one α-helix (Fig. 1c). The β-strands in each subdomain, connected by loops, form a twisted antiparallel β-sheet. The N-terminal region, the sole α-helix of the P1 subdomain, and the two long antiparallel β-strands in the barrel-like β-sheet structure of the P2 subdomain contribute significantly to the dimeric interactions. The C-terminal region of the P1 subdomain faces the hollows at the fivefold and quasi-sixfold axes in the T=3 capsid structure. The rectangular-shaped top surface of the P domain dimer is essentially flat except for two shallow depressions on the sides close to the dimeric interface but away from the dimeric twofold axis (Fig. 1c, rectangular box).

Structure of the P Domain–H-Type 1 Complex.

The electron-density map (2FoFc) of the P domain–H-type 1 complex, obtained immediately after the MR and in the early stages of refinement, showed the extra density due to the bound carbohydrate residues at the same contour level (1σ) as the protein (Fig. 2a). All of the five carbohydrate moieties were easily modeled into the electron-density map and well behaved in the refinement. The H-type 1 pentasaccharide binds to a surface-exposed shallow depression at the top (in relation to its location in the capsid) of the P domain with its two terminal residues, α-Fuc and β-Gal, anchored to the binding site and the rest of the ligand projecting outward. The binding site is lined by a constellation of hydrogen-bond donors and acceptors that interact with four bound water molecules in the unliganded state (Fig. 2b). The binding of the ligand results in the displacement of these bound water molecules, providing a favorable entropic effect, and the formation of seven new hydrogen bonds between the exocyclic hydroxyl groups of the two carbohydrate residues and the P domain residues. These residues include a combination of charged and neutral side chains from Gln-342, Asp-344, His-329, Ser-377, and Asp-327, and a main chain carbonyl group of Pro-378 (Fig. 2c). The first three amino acid residues interact with α-Fuc and the remaining with β-Gal. The precise geometric arrangement of the side chains of these residues allow 3-OH and 4-OH of β-Gal to engage in a cooperative hydrogen bonding in which these hydroxyls simultaneously act as donors and acceptors (Fig. 2c and Fig. S4). For example, the 3-OH of β-Gal serves as a hydrogen-bond donor to the carboxylate of Asp-327 and an acceptor from the polar side chains of His-329 and Ser-377. The CH of α-Fuc at positions C1 and C2 of the hexose ring are positioned in close proximity (≈4 Å) to the indole ring of Trp-375, indicating possible hydrophobic interactions (Fig. 2c and Fig. S4). Involvement of only the terminal fucose and galactose of the H type 1 in the binding is consistent with the observation that NV also interacts with other HBGAs that have the same two carbohydrates as terminal residues, such as H-types 2 and 3, Ley, and Leb (11, 12).

Fig. 2.
NV P domain–HBGA interactions. (a) The electron density (1σ level) of the bound pentasaccharide corresponding to H-type 1 HBGA in the 2FoFc map obtained after MR and before any refinement clearly showed all of the five sugar ...

Structure of the P Domain–A-Type HBGA Complex.

The electron-density map (2FoFc) of the P domain–A-type complex obtained after MR, as with the H-type 1 complex, revealed all of the three carbohydrate residues (Fig. S2). The A-type trisaccharide binds to the same site in the P domain as the H-type 1, forming an extensive network of hydrogen-bond interactions with the P domain residues. The A-type differs from H-type 1 by having an N-acetyl-galactosamine (GalNAc) residue attached to the β-Gal through a α1–3 linkage (Fig. 2 and Fig. S1). This addition is catalyzed by the glycosyltransferase A enzyme, which is functional in individuals with type A blood (13).

In the A-type trisaccharide, the terminal GalNAc and α-Fuc moieties that are attached to the central β-Gal make all of the contacts with the P domain (Fig. 2d). The central β-Gal is not involved in any interactions. The hexose ring of the GalNAc occupies the same position as the penultimate β-Gal residue of the H-type 1 with essentially the same cooperative hydrogen-bond interactions involving its hydroxyl groups and the side chains of Ser-377, Asp-327, and His-329, and backbone carbonyl oxygen of Pro-378. As a result, the acetamido group of the GalNAc is positioned in the same direction as the α-Fuc attached to β-Gal of the H-type 1 HBGA. The methyl group of the acetamido moiety, similar to the α-Fuc in H-type 1, makes hydrophobic contact with Trp-375 (Fig. 2d and Fig. S5). In addition, the NH of the acetamido group participates in a hydrogen-bond interaction with Asp-327 via two water molecules (Fig. 2d and Fig. S5). One of these water molecules, which hydrogen-bonds to the side chain of Asp-327, is part of the hydration shell of the P domain because it is present in the unliganded P domain structure. The other bridging water molecule, present only in the liganded structure, hydrogen-bonds to NH of the acetamido group (Fig. 2d). The α-Fuc residue attached to the C2 of the central β-Gal of the A-type HBGA and positioned on the side opposite to that of the acetamido group makes two hydrogen bonds: one directly with the side chain of Ser-380, and another with the side chain of Asp-346 mediated by a water molecule (Fig. S5). Based on the location of the central β-Gal residue, the proximal carbohydrate groups in an A-type HBGA would project out similar to that seen with the H-type 1 carbohydrate.

Structural Basis of Specific Recognition of H-Type 1 and A-Type HBGA by NV.

In the binding of H-type 1 and A-type HBGAs, the cooperative hydrogen bonding involving 3-OH and 4-OH of the galactose moiety is conserved (Fig. 2). Such highly precise cooperative hydrogen bonding contributes significantly to both the specificity and the stability of carbohydrate binding (23). However, these interactions alone are not sufficient to confer specificity based on the available binding data. For instance, NV binds to H-types 2 and 3, and Lewis blood group antigen Leb, but not to Lea (11, 20). The main difference between the Lea and other H-type HBGAs is that Lea does not have the terminal fucose residue (Fig. S1). Furthermore, NV does not bind the B-type HBGA, which differs from the A-type by having a terminal α-Gal instead of GalNAc. From our structural analysis, a common factor in carbohydrate binding, in addition to the conserved hydrogen-bonding interactions, is the hydrophobic interaction involving Trp-375, either with the terminal α-Fuc of the H-type 1 or with the acetamido group of GalNAc of the A-type, suggesting that such a hydrophobic interaction plays a critical role in conferring specificity. The cooperative hydrogen-bond interactions between the P domain residues and the hydroxyl groups of the galactose precisely position the attached fucose (in H-type 1) or the acetamido group (in A-type) for hydrophobic interactions with Trp-375. Along with Trp-375, all of the amino acid residues of the P domain that hydrogen-bond with exocyclic hydroxyls of β-Gal (H-type 1) and GalNAc (A-type) are remarkably well conserved across GI NoVs (Fig. 3a), suggesting a very similar HBGA binding pattern for the majority of GI NoVs. However, the P domain residues, which hydrogen-bond to the α-Fuc of the H-type 1 or the acetamido group of the A-type, show some variation, indicating that these residues may be responsible for modulating the differential affinities of these HBGAs for GI NoVs.

Fig. 3.
HBGA binding sites in GI and GII NoVs are different. (a) Structure-based sequence comparison of the NV (GI) and VA387 (GII) noroviruses, first two rows, in the P2 domain showing that carbohydrate binding amino acid residues are not conserved in these ...

His–Trp Cation–π Interaction.

In addition to the hydrogen-bond and hydrophobic interactions, another important interaction that could influence carbohydrate binding is the face-to-face stacking interaction observed between the side chains of His-329 and Trp-375 (Fig. 2). Such a stacking between the positively charged imidazolium ring of the His and the Trp indole ring, representing a cation–π interaction prevalent in many protein structures and protein–ligand interactions (24), increases the pKa of the imidazolium and thereby insures a charged-neutral hydrogen bond with 3-OH of β-Gal. Mutation of either one of these residues to Ala completely abrogates carbohydrate binding by the NV capsid as shown by studies using surface plasmon resonance (Fig. 4). These studies were carried out with recombinant VLPs after ensuring that these point mutations did not interfere with the capsid formation by examining their morphology by electron microscopy. These studies also provide evidence that the HBGA binding site observed in the P domain construct used in our structural studies is preserved in the context of the capsid structure, and that the capsid protein has a single binding site for HBGAs.

Fig. 4.
Norwalk virus-like particle (VLP) binding to immobilized H-type 1, A, and B trisaccharide carbohydrates detected by surface plasmon resonance. Wild-type NV VLPs bound H-type 1 and A but not B carbohydrates. Point mutant NV VLPs H329A and W375A maintain ...

HBGA Binding Site in GI Viruses Is Different from That in GII Viruses.

Although the amino acid residues involved in the HBGA recognition are well conserved among GI NoVs, none of these residues is conserved in the GII NoVs (Fig. 3a). This is consistent with the observations that GII viruses exhibit a different pattern of binding specificity for HBGAs and further indicates that these viruses have a HBGA binding site that could be structurally dissimilar to GI viruses. Recently, x-ray structures of the P domain of a GII NoV (VA387) in complex with A- and B-type trisaccharides at a resolution of ≈2.1 Å were reported (21). Despite similar S and P domain organization and polypeptide fold, the carbohydrate binding site in the GII P domain is distinctly different both in its location and in its structural characteristics. For instance, the binding site in the GII P domain does not have a Trp–His interaction (Fig. 3b). The reported GII binding site is predominantly formed by residues from two surface-exposed loops that are close to the P domain dimeric interface, in contrast to the GI binding site located on the other side of the P domain formed by residues that project from a well structured antiparallel β-sheet (Fig. 3 b and c). In the GII VA387 NoV, the majority of the interactions with either A- or B-type carbohydrates involve only the terminal nondiscriminatory fucosyl moiety. As with GI, the amino acid residues implicated in the GII binding site are well conserved, and both of these sets of residues form distinct class-specific clusters consistent with the predictions from the evolutionary trace analysis of NoV sequences (25).

In conclusion, we have provided an atomic-resolution characterization of how Norwalk virus, the prototype GI norovirus, recognizes HBGAs, and described the interactions responsible for the binding specificity. The location of the carbohydrate binding site at the distal surface of the capsid, and the orientation of the bound carbohydrates projecting out from the surface of the NV strongly substantiate the possible role of HBGAs in initiating cell attachment. Recent studies, however, indicate that interactions with HBGAs alone may not be sufficient, and an additional receptor(s) are likely necessary for NV internalization into cells (26). The observation that GI and GII NoVs use distinctly different epitopes for binding to HBGAs support the idea that these two genogroups may have diverged early and coevolved in human subpopulations depending upon blood type distribution (18). Our studies provide a molecular explanation for why the HBGA binding pattern exhibited by GI is restricted compared with the more permissive binding pattern exhibited by GII NoVs. In the former, as exemplified in NV, the carbohydrate binding site with precisely positioned side chains from a structurally stable part of the P2 subdomain is optimally configured to primarily recognize a terminal Gal-Fuc or Gal-acetamido (GalNAc) combination through well coordinated hydrogen-bond and hydrophobic interactions, thus limiting the number of HBGAs with which these NoVs can interact. In contrast, based on the structural analysis of VA387 (21), GII viruses primarily recognize only the terminal fucose moiety, a common terminal carbohydrate residue in many of the HBGAs. This perhaps is the reason why GII NoVs are more prevalent, although not necessarily more pathogenic, in human populations.

Methods

Expression, Purification, and Crystallization of NV P-Domain.

The P-domain (amino acids 225–519) construct with N-terminal His6–MBP (maltose binding protein) tag was cloned into an expression vector pMal-C2E (New England Biolabs) with a TEV (tobacco etch virus) cleavage site between MBP and the P domain, and expressed in BL-21 (DE3) E. coli (Novagen) cells. The His–MBP-tagged P domain was first purified over a Ni-NTA (Qiagen) column, and the His–MBP tag was removed by using TEV protease, which was produced by using Addgene plasmid 8827 according to the protocol described in ref. 27. The P domain was then separated from His–MBP by rerunning the mixture through another Ni-NTA column, and purified further by size-exclusion chromatography, which clearly showed a single peak corresponding to the P domain dimer. The P domain was concentrated and stored in 10 mM Tris·HCl (pH 7.5)/150 mM NaCl/1 mM DTT/5 mM MgCl2/5 mM CaCl2.

Crystals of the unliganded and the liganded P domain were obtained by the hanging-drop vapor diffusion method at 20°C with 50 mM NaAc (pH 4.8)/0.2 M ammonium nitrate/20% PEG 3350 (protein concentration ≈3.5 mg/ml). The P domain was cocrystallized in the presence of H-type 1 pentasaccharide (purchased from Dextra Laboratories) or the A-type trisaccharide (purchased from Sigma) with a 1:60 (protein to ligand) molar ratio. The cryoprotectant for all of the three crystals was 20% glycerol reconstituted with mother liquor.

Diffraction Data Collection, Structure Determination, and Refinement.

Diffraction data for the unliganded and liganded P domain crystals were collected on the SBC-CAT 19ID beamline (Argonne National Laboratory) at a wavelength of 0.9792 Å, using 0.5° oscillation angle, and processed by using HKL2000 (28). The structures were determined by molecular replacement (MR) techniques with PHASER (29) as implemented in the CCP4 package (30), using the P domain dimer from the previously published NV capsid structure at 3.4-Å resolution (PDB entry 1IHM) as a search model (8). After MR, iterative cycles of model building by using COOT (31), map improvement including incorporation of solvent by using ARP/wARP (32), and refinement by using REFMAC5 (33) were carried out. Five percent of the data were set aside for Rfree calculations (34). The oligosaccharide moieties were modeled into the electron density by using the monomer sketcher module of the CCP4 suite and COOT. During the course of the refinement, and after the final refinement, stereochemistry of the structures was checked by using PROCHECK (35).

Surface Plasmon Resonance Detection of NV VLP Binding Carbohydrates.

A streptavidin-coated Biacore microfluidics sensor chip SA was prepared as suggested by the manufacturer (Biacore). Multivalent carbohydrate reagents (H-type 1, A, and B trisaccharides) with the carbohydrate moieties and the biotin covalently linked to polyacrylamide (Glycotech) were injected at 10 μg/ml, 1 μl/min, for 5 min and 0.1 μg/ml, 1 μl/min, for 5 min, respectively, and were immobilized on the sensor chip SA, giving an increase in relative refraction units (RU) of 1,150.5 and 160, respectively. Unbound streptavidin was blocked by injection of free biotin (Sigma). Recombinant NV VLPs, H229A and W375A mutant VLPs (see SI Materials and Methods) were injected over the sensor chip SA at 100 μg/ml, 5 μl/min for 20 min, and binding was detected as increasing relative RU. Regeneration of the sensor chip SA was achieved with 5 μl/min for 1 min of 0.5 M glycine (Bio-Rad), pH 10, followed by 0.5 M glycine, pH 2, then 0.5 M glycine, pH 10 again. Surface performance tests of the sensor chip SA with immobilized carbohydrate indicated that the baseline RU and VLP binding were stable, which indicated that the immobilized carbohydrate ligand was not removed by regeneration and that the amount of VLP analyte removed from the carbohydrate ligand by regeneration was repeatable and consistent. The multivalent nature of the VLPs and immobilized carbohydrate did not allow analysis of binding constants or kinetics. Relative binding can be compared between different carbohydrates and different VLPs. Similar carbohydrate binding results were obtained with enzyme-linked immunosorbent-based carbohydrate microtiter plate binding assay (data not shown and ref. 11).

Coordinates and structure factors for the three structures discussed in this manuscript have been deposited in the Protein Data Bank with PDB ID codes of 2ZL5, 2ZL6, and 2ZL7.

Supplementary Material

Supporting Information:

Acknowledgments.

We thank Robert Atmar and Florante Quiocho for many helpful discussions and critical reading of the manuscript, and Jennifer Fallon for technical advice. We acknowledge the use of the CAMD (Baton Rouge, Louisiana) and SBC-CAT 19ID synchrotron beamlines for diffraction data collection and thank their staff for excellent help. This work was supported by National Institutes of Health Grants P01 AI057788 (to M.K.E. and B.V.V.P.), T32 DK07664 (to A.M.H.), and P30 DK56330, and by a grant from the Robert Welch Foundation (to B.V.V.P.). The SBC-CAT 19ID beamline at the Advanced Photon Source is supported by the U.S. Department of Energy, Basic Energy Sciences, Office of Science, under Contract W-31-109-Eng-38.

Footnotes

The authors declare no conflict of interest.

Data deposition: The atomic coordinates have been deposited in the Protein Data Bank, www.pdb.org (PDB ID codes 2ZL5, 2ZL6, and 2ZL7).

This article contains supporting information online at www.pnas.org/cgi/content/full/0803275105/DCSupplemental.

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