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Structures of B-lymphotropic polyomavirus VP1 in complex with oligosaccharide ligands.

Neu U, Khan ZM, Schuch B, Palma AS, Liu Y, Pawlita M, Feizi T, Stehle T - PLoS Pathog. (2013)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany.

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.

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Specific interactions of LPyV VP1 and 3SL.A and B. LPyV VP1 is shown in cartoon and surface representation, with side chains interacting with 3SL shown in stick representation. The 3SL oligosaccharide is shown in stick representation and colored by element, with carbons in orange, nitrogens in blue and oxygens in red. Waters are represented with spheres. Selected carbon atoms of 3SL are numbered in italics. Residues engaging in hydrophobic interactions with 3SL are colored bright green and residues forming polar van der Waals contacts or water-mediated hydrogen bonds are colored dark green. Direct hydrogen bonds between LPyV VP1 and the oligosaccharide are shown as red dashed lines, water-mediated hydrogen bonds are colored black. The views depicted in A and B differ by a 70° rotation around a vertical axis. C. Location of LPyV VP1 mutations influencing cell tropism. An entire LPyV VP1 pentamer is shown in surface representation. The N-terminal arms were omitted for clarity. One monomer is colored dark green, and the residues forming the oligosaccharide binding site are highlighted in light green. Residues whose mutation was shown to influence cell tropism of LPyV VP1 are colored magenta. The 3SL and 3SLN oligosaccharides are shown in stick representation and colored orange and yellow, respectively.
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ppat-1003714-g003: Specific interactions of LPyV VP1 and 3SL.A and B. LPyV VP1 is shown in cartoon and surface representation, with side chains interacting with 3SL shown in stick representation. The 3SL oligosaccharide is shown in stick representation and colored by element, with carbons in orange, nitrogens in blue and oxygens in red. Waters are represented with spheres. Selected carbon atoms of 3SL are numbered in italics. Residues engaging in hydrophobic interactions with 3SL are colored bright green and residues forming polar van der Waals contacts or water-mediated hydrogen bonds are colored dark green. Direct hydrogen bonds between LPyV VP1 and the oligosaccharide are shown as red dashed lines, water-mediated hydrogen bonds are colored black. The views depicted in A and B differ by a 70° rotation around a vertical axis. C. Location of LPyV VP1 mutations influencing cell tropism. An entire LPyV VP1 pentamer is shown in surface representation. The N-terminal arms were omitted for clarity. One monomer is colored dark green, and the residues forming the oligosaccharide binding site are highlighted in light green. Residues whose mutation was shown to influence cell tropism of LPyV VP1 are colored magenta. The 3SL and 3SLN oligosaccharides are shown in stick representation and colored orange and yellow, respectively.

Mentions: The linear 3SL and 3SLN chains can assume a range of possible conformations in solution due to rotational freedom of the glycosidic bonds [26], [27]. LPyV VP1 binds both compounds in a conformation of the Neu5Ac-α2,3-Gal linkage that is preferred in solution (mean torsion angles 65°, −26°) [26], [27]. The terminal Neu5Ac residue, which is best defined by electron density and has low temperature factors (B-factors), inserts deeply into a cleft and engages the protein with multiple contacts (Fig. 3A,B). The adjacent Gal makes fewer contacts and has elevated B-factors. The terminal Glc and GlcNAc residues of 3SL and 3SLN have the weakest electron density and are only visible in the best occupied sites in each structure (Fig. 2B,C).


Structures of B-lymphotropic polyomavirus VP1 in complex with oligosaccharide ligands.

Neu U, Khan ZM, Schuch B, Palma AS, Liu Y, Pawlita M, Feizi T, Stehle T - PLoS Pathog. (2013)

Specific interactions of LPyV VP1 and 3SL.A and B. LPyV VP1 is shown in cartoon and surface representation, with side chains interacting with 3SL shown in stick representation. The 3SL oligosaccharide is shown in stick representation and colored by element, with carbons in orange, nitrogens in blue and oxygens in red. Waters are represented with spheres. Selected carbon atoms of 3SL are numbered in italics. Residues engaging in hydrophobic interactions with 3SL are colored bright green and residues forming polar van der Waals contacts or water-mediated hydrogen bonds are colored dark green. Direct hydrogen bonds between LPyV VP1 and the oligosaccharide are shown as red dashed lines, water-mediated hydrogen bonds are colored black. The views depicted in A and B differ by a 70° rotation around a vertical axis. C. Location of LPyV VP1 mutations influencing cell tropism. An entire LPyV VP1 pentamer is shown in surface representation. The N-terminal arms were omitted for clarity. One monomer is colored dark green, and the residues forming the oligosaccharide binding site are highlighted in light green. Residues whose mutation was shown to influence cell tropism of LPyV VP1 are colored magenta. The 3SL and 3SLN oligosaccharides are shown in stick representation and colored orange and yellow, respectively.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3814675&req=5

ppat-1003714-g003: Specific interactions of LPyV VP1 and 3SL.A and B. LPyV VP1 is shown in cartoon and surface representation, with side chains interacting with 3SL shown in stick representation. The 3SL oligosaccharide is shown in stick representation and colored by element, with carbons in orange, nitrogens in blue and oxygens in red. Waters are represented with spheres. Selected carbon atoms of 3SL are numbered in italics. Residues engaging in hydrophobic interactions with 3SL are colored bright green and residues forming polar van der Waals contacts or water-mediated hydrogen bonds are colored dark green. Direct hydrogen bonds between LPyV VP1 and the oligosaccharide are shown as red dashed lines, water-mediated hydrogen bonds are colored black. The views depicted in A and B differ by a 70° rotation around a vertical axis. C. Location of LPyV VP1 mutations influencing cell tropism. An entire LPyV VP1 pentamer is shown in surface representation. The N-terminal arms were omitted for clarity. One monomer is colored dark green, and the residues forming the oligosaccharide binding site are highlighted in light green. Residues whose mutation was shown to influence cell tropism of LPyV VP1 are colored magenta. The 3SL and 3SLN oligosaccharides are shown in stick representation and colored orange and yellow, respectively.
Mentions: The linear 3SL and 3SLN chains can assume a range of possible conformations in solution due to rotational freedom of the glycosidic bonds [26], [27]. LPyV VP1 binds both compounds in a conformation of the Neu5Ac-α2,3-Gal linkage that is preferred in solution (mean torsion angles 65°, −26°) [26], [27]. The terminal Neu5Ac residue, which is best defined by electron density and has low temperature factors (B-factors), inserts deeply into a cleft and engages the protein with multiple contacts (Fig. 3A,B). The adjacent Gal makes fewer contacts and has elevated B-factors. The terminal Glc and GlcNAc residues of 3SL and 3SLN have the weakest electron density and are only visible in the best occupied sites in each structure (Fig. 2B,C).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany.

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.

Show MeSH
Related in: MedlinePlus