Structures of B-Lymphotropic Polyomavirus VP1 in Complex with Oligosaccharide Ligands

Abstract

B-Lymphotropic Polyomavirus (LPyV) serves as a paradigm of virus receptor binding and tropism, and is the closest relative of the recently discovered Human Polyomavirus 9 (HPyV9). LPyV infection depends on sialic acid on host cells, but the molecular interactions underlying LPyV-receptor binding were unknown. We find by glycan array screening that LPyV specifically recognizes a linear carbohydrate motif that contains α2,3-linked sialic acid. High-resolution crystal structures of the LPyV capsid protein VP1 alone and in complex with the trisaccharide ligands 3′-sialyllactose and 3′-sialyl-N-acetyl-lactosamine (3SL and 3SLN, respectively) show essentially identical interactions. Most contacts are contributed by the sialic acid moiety, which is almost entirely buried in a narrow, preformed cleft at the outer surface of the capsid. The recessed nature of the binding site on VP1 and the nature of the observed glycan interactions differ from those of related polyomaviruses and most other sialic acid-binding viruses, which bind sialic acid in shallow, more exposed grooves. Despite their different modes for recognition, the sialic acid binding sites of LPyV and SV40 are half-conserved, hinting at an evolutionary strategy for diversification of binding sites. Our analysis provides a structural basis for the observed specificity of LPyV for linear glycan motifs terminating in α2,3-linked sialic acid, and links the different tropisms of known LPyV strains to the receptor binding site. It also serves as a useful template for understanding the ligand-binding properties and serological crossreactivity of HPyV9.

Crystallographic and Glycan Microarray Analysis of Human Polyomavirus 9 VP1 Identifies N -Glycolyl Neuraminic Acid as a Receptor Candidate

“…1). Little or weak binding to glycosylceramides GM3 and GM3(Gc) by both proteins is consistent with the finding in our recent study of LPyV VP1 using a different array set (31). It should be noted that no signals of binding to longer oligosaccharide sequences with the trisaccharide 3SLN terminus, such as probe LSTd.DH (probe 27), were detected with HPyV9 VP1.…”

“…We hypothesized that HPyV9 might interact with sialic acids on the basis of its similarity to LPyV, which binds to sialylated oligosaccharides (31). However, the residues in the sialic acid binding region of the LPyV VP1 are less conserved in HPyV9 of VP1.…”

“…The probes are listed in Table 1 and were arrayed at four levels: 0.3, 0.8, 1.7, and 5.0 fmol/spot. The microarray analysis was performed essentially as described previously (27,31). In brief, microarrays were blocked in 5 mM HEPES (pH 7.4), 150 mM NaCl, 3% (wt/vol) bovine serum albumin (BSA; Sigma), and 5 mM CaCl 2 (referred to as HBS-BSA).…”

“…VP1 is the major polyomavirus capsid protein, and a collection of available VP1 structures from different polyomaviruses shows that the protein adopts a jelly roll fold and assembles into a homopentamer around a central cavity (24)(25)(26)(27)(28)(29)(30)(31). While the pentameric core structure is conserved in all VP1 proteins, these structures from different polyomaviruses exhibit substantial differences in the sequence, length, and conformation of their surface-exposed loops.…”

“…These highly variable regions contain the sites for receptor engagement (25)(26)(27)29) as well as antibody binding (21)(22)(23)32). All human polyomavirus VP1 structures known to date engage glycans terminating in 5-N-acetyl neuraminic acid (Neu5Ac) as receptors (27,(29)(30)(31), with, in some cases, drastically different interactions taking place.…”