Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comparative Study
. 2014 Jun;88(11):6100-11.
doi: 10.1128/JVI.03455-13. Epub 2014 Mar 19.

Crystallographic and glycan microarray analysis of human polyomavirus 9 VP1 identifies N-glycolyl neuraminic acid as a receptor candidate

Zaigham Mahmood Khan  1 , Yan Liu, Ursula Neu, Michel Gilbert, Bernhard Ehlers, Ten Feizi, Thilo Stehle
Affiliations
Comparative Study

Crystallographic and glycan microarray analysis of human polyomavirus 9 VP1 identifies N-glycolyl neuraminic acid as a receptor candidate

Zaigham Mahmood Khan et al. J Virol. 2014 Jun.

Abstract

Human polyomavirus 9 (HPyV9) is a closely related homologue of simian B-lymphotropic polyomavirus (LPyV). In order to define the architecture and receptor binding properties of HPyV9, we solved high-resolution crystal structures of its major capsid protein, VP1, in complex with three putative oligosaccharide receptors identified by glycan microarray screening. Comparison of the properties of HPyV9 VP1 with the known structure and glycan-binding properties of LPyV VP1 revealed that both viruses engage short sialylated oligosaccharides, but small yet important differences in specificity were detected. Surprisingly, HPyV9 VP1 preferentially binds sialyllactosamine compounds terminating in 5-N-glycolyl neuraminic acid (Neu5Gc) over those terminating in 5-N-acetyl neuraminic acid (Neu5Ac), whereas LPyV does not exhibit such a preference. The structural analysis demonstrated that HPyV9 makes specific contacts, via hydrogen bonds, with the extra hydroxyl group present in Neu5Gc. An equivalent hydrogen bond cannot be formed by LPyV VP1.

Importance: The most common sialic acid in humans is 5-N-acetyl neuraminic acid (Neu5Ac), but various modifications give rise to more than 50 different sialic acid variants that decorate the cell surface. Unlike most mammals, humans cannot synthesize the sialic acid variant 5-N-glycolyl neuraminic acid (Neu5Gc) due to a gene defect. Humans can, however, still acquire this compound from dietary sources. The role of Neu5Gc in receptor engagement and in defining viral tropism is only beginning to emerge, and structural analyses defining the differences in specificity for Neu5Ac and Neu5Gc are still rare. Using glycan microarray screening and high-resolution protein crystallography, we have examined the receptor specificity of a recently discovered human polyomavirus, HPyV9, and compared it to that of the closely related simian polyomavirus LPyV. Our study highlights critical differences in the specificities of both viruses, contributing to an enhanced understanding of the principles that underlie pathogen selectivity for modified sialic acids.

PubMed Disclaimer

Figures

FIG 1
FIG 1
Glycan microarray screening of HPyV9 VP1 (A) and LPyV VP1 (B) using 28 lipid-linked oligosaccharide probes. Each oligosaccharide probe was arrayed at four levels (as indicated) in duplicate. The complete list of probes and their sequences are provided in Table 1. Numerical scores of the binding signals are shown as the means of the fluorescence intensities of duplicate spots with error bars, which represent half of the difference between the two values. Cer, natural glycolipids with various ceramide moieties; DH, neoglycolipids (NGLs) prepared from reducing oligosaccharides by reductive amination with the amino lipid 1,2-dihexadecyl-sn-glycero-3-phosphoethanolamine (DHPE).
FIG 2
FIG 2
Structure of HPyV9 VP1 in complex with sialyloligosaccharides. (A) HPyV9 VP1 pentamer structure in complex with 3SLN. The pentamer is shown in cartoon representation, with one VP1 monomer highlighted in chocolate color and the other monomers shown in gray. The β strands (Anew, B to I) are labeled. 3SLN is drawn as a stick model and colored according to atom type (blue, nitrogens; red, oxygens; gold, carbons). One calcium ion is bound to each VP1 monomer, and the ions bound to the colored VP1 monomer are shown as green spheres, with the protein residues contacting it shown in stick representation. (B and C) Close-up views of the 3SLN (B) and 3GSLN (C) binding sites. HPyV9 VP1 and 3SLN are drawn as described for panel A, while the carbon atoms are colored yellow for 3GSLN. The view is adjusted to show more clearly the trisaccharide with the associated VP1 loops (the BC1, DE, and HI loops) of one monomer and the BC2 loop of the clockwise (cw) monomer. Composite-annealed omit difference density maps are shown contoured at 2.5σ around glycan at a 2.1-Å radius.
FIG 3
FIG 3
Interactions between HPyV9 VP1 and sialyloligosaccharides. (A and B) Interactions between HPyV9 VP1 and 3SLN. The main chain of HPyV9 VP1 is shown in cartoon representation. One monomer is shown in chocolate color, while other monomers are shown in gray. The amino acid side chains interacting with 3SLN are shown as sticks, and the corresponding C-α atoms are shown as spheres. The backbone amide and carbonyl groups are shown only when engaging the oligosaccharide. 3SLN is shown as in Fig. 2B. Water molecules are represented as red spheres. Hydrogen bonds are shown as black dashed lines. The view in panel A was rotated by about 90° along a vertical axis to obtain the view presented in panel B. (C) Interactions between HPyV9 VP1 and 3GSLN. HPyV9 VP1 is drawn as described for panel A; the ligand 3GSLN is shown as in Fig. 2C. Residues H274 and N282, which interact specifically with the hydroxymethyl chain of Neu5Gc, are shown in stick representation.
FIG 4
FIG 4
Comparison of the sialyloligosaccharide binding pockets of HPyV9 and LPyV VP1 proteins. (A) The structure of HPyV9 VP1-3SLN is superimposed onto the structure of LPyV VP1-3SLN (PDB accession number 4MBZ). HPyV9 VP1 and 3SLN are shown as in Fig. 3. For LPyV VP1, one monomer is shown in forest green and other monomers are shown in gray. The side chains are shown in stick representation, and the corresponding C-α atoms are shown as spheres. The 3SLN bound to LPyV VP1 is shown in stick representation; nitrogen and oxygen atoms are colored blue and red, respectively, and carbon atoms are colored forest green. Only residues forming contacts with 3SLN that differ between the two viruses are shown. Water molecules are represented as red and orange spheres for HPyV9 and LPyV, respectively. Hydrogen bonds are shown as black and green dashed lines for HPyV9 and LPyV, respectively. The 5-fold axis of the VP1 pentamer is indicated to depict the orientation of the superimposed pentamers. (B) The structure of HPyV9 VP1-3GSLN is superimposed onto the structure of LPyV VP1-3SLN (PDB accession number 4MBZ). HPyV9 VP1 and 3GSLN are shown as in Fig. 3C. LPyV VP1 and 3SLN are shown as described for panel A. Histidine is present in the binding sites of both viruses (H274 in HPyV9 and H271 in LPyV), but only in HPyV9 does it coordinate the hydroxyl group of Neu5Gc, which also interacts with the side chain of N282 of HPyV9 VP1. Hydrogen bonds are shown as black dashed lines. D71 is present in the proximal vicinity and stabilized the side chain of the N282 via a hydrogen bond (red dashed line).
FIG 5
FIG 5
Comparison of binding of the wild-type HPyV9 VP1 (A) and the mutant HPyV9 VP1 (B) to lipid-linked oligosaccharide probes (3SLN.DH and 3GSLN.DH) in microarray analyses. Both probes were arrayed at four levels (as indicated) in duplicate. Numerical scores of the binding signals are shown as the means of the fluorescence intensities of duplicate spots with error bars, which represent half of the difference between the two values. The wt and mutant HPyV9 VP1 proteins were analyzed in parallel at 150 μg/ml precomplexed with anti-His and biotin–anti-mouse IgG antibodies.
FIG 6
FIG 6
Structural representation of serological cross-reactivity and antigenicity of polyomaviruses. (A) Pairwise comparison of the apical surfaces of HPyV9 VP1 and LPyV VP1 (PDB accession number 4MBZ) pentamers. The apical surfaces of VP1 are shown in surface representation. Identical amino acids between these two viruses are colored gray. Nonidentical amino acids between the two viruses are colored chocolate and forest green for HPyV9 and LPyV, respectively. The glycan ligand (3SLN) is shown in stick representation, as in Fig. 3. (B) Pairwise comparison of the apical surfaces of HPyV9 VP1 and MCPyV VP1 (PDB accession number 4FMI) pentamers. The apical surfaces are shown in surface representation. Identical amino acids between the two viruses are colored gray. Nonidentical amino acids between the two viruses are colored chocolate and cyan for HPyV9 and MCPyV, respectively. The glycan ligand (3SLN) is shown in stick representation, as in Fig. 3.
FIG 7
FIG 7
Comparison of Neu5Gc binding sites. Recognition of Neu5Gc by HPyV9 VP1 (A), Shiga-toxigenic E. coli SubB (PDB accession number 3DWP) (B), and porcine rotavirus strain CRW-8 VP8 (PDB accession number 3TAY) (C). The proteins are shown in surface representation. Neu5Gc is shown as in Fig. 4B. The critical amino acids making hydrogen bonds (black dashed lines) with Neu5Gc are shown in stick representation, and associated C-α atoms are shown as spheres. The water molecule in panel C is shown as a red sphere. The extra hydroxyl group of Neu5Gc makes two hydrogen bonds in each case.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Neu U, Stehle T, Atwood WJ. 2009. The Polyomaviridae: contributions of virus structure to our understanding of virus receptors and infectious entry. Virology 384:389–399. 10.1016/j.virol.2008.12.021 - DOI - PMC - PubMed
    1. Padgett BL, Walker DL, ZuRhein GM, Eckroade RJ, Dessel BH. 1971. Cultivation of papova-like virus from human brain with progressive multifocal leucoencephalopathy. Lancet i:1257–1260 - PubMed
    1. Gardner SD, Field AM, Coleman DV, Hulme B. 1971. New human papovavirus (B.K.) isolated from urine after renal transplantation. Lancet i:1253–1257 - PubMed
    1. Allander T, Andreasson K, Gupta S, Bjerkner A, Bogdanovic G, Persson MA, Dalianis T, Ramqvist T, Andersson B. 2007. Identification of a third human polyomavirus. J. Virol. 81:4130–4136. 10.1128/JVI.00028-07 - DOI - PMC - PubMed
    1. Gaynor AM, Nissen MD, Whiley DM, Mackay IM, Lambert SB, Wu G, Brennan DC, Storch GA, Sloots TP, Wang D. 2007. Identification of a novel polyomavirus from patients with acute respiratory tract infections. PLoS Pathog. 3:e64. 10.1371/journal.ppat.0030064 - DOI - PMC - PubMed

Publication types