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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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Comparison of oligosaccharide binding sites of LPyV and SV40.A & C. LPyV VP1 in complex with 3SL. B & D. SV40 VP1 in complex with GM1 pdb (3BWR). In panels A and B, the proteins are shown in surface representation, with the BC- and HI-loops also indicated in cartoon representation. Residues contributing to ligand binding or specificity are shown in stick representation. Receptor-binding residues that are identical between the two proteins are colored yellow in both panels, while residues that differ between the two proteins, but reside on the same location on the VP1 surface, are colored bright green for LPyV and cyan for SV40. Residues that make additional contacts with the oligosaccharide only in one complex are colored dark green for LPyV and dark blue for SV40. Their non-binding counterparts in the other complex are colored white. The carbohydrate ligands are shown as orange sticks. Hydrogen bonds and water-mediated hydrogen bonds are shown as black and grey dashes, respectively. In panels C and D, the proteins are shown in ribbon presentation, with one monomer highlighted in green for LPyV and blue for SV40 VP1, respectively.
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ppat-1003714-g005: Comparison of oligosaccharide binding sites of LPyV and SV40.A & C. LPyV VP1 in complex with 3SL. B & D. SV40 VP1 in complex with GM1 pdb (3BWR). In panels A and B, the proteins are shown in surface representation, with the BC- and HI-loops also indicated in cartoon representation. Residues contributing to ligand binding or specificity are shown in stick representation. Receptor-binding residues that are identical between the two proteins are colored yellow in both panels, while residues that differ between the two proteins, but reside on the same location on the VP1 surface, are colored bright green for LPyV and cyan for SV40. Residues that make additional contacts with the oligosaccharide only in one complex are colored dark green for LPyV and dark blue for SV40. Their non-binding counterparts in the other complex are colored white. The carbohydrate ligands are shown as orange sticks. Hydrogen bonds and water-mediated hydrogen bonds are shown as black and grey dashes, respectively. In panels C and D, the proteins are shown in ribbon presentation, with one monomer highlighted in green for LPyV and blue for SV40 VP1, respectively.

Mentions: Despite these differences, the LPyV binding site lies in a region that partially overlaps with the sialic acid binding sites on other polyomaviruses. LPyV engages Neu5Ac in an orientation that resembles that seen in the complex of SV40 VP1 with GM1, and it is therefore useful to compare the two modes of interaction (Fig. 5). Interestingly, the two binding sites are “half-conserved”. The HI-loop, which contributes the “back” wall of the sialic acid binding site, is conserved, while the BC1-, BC2cw- and DE-loops feature marked differences, which explain the different orientations of bound Neu5Ac. In the SV40 VP1 complex, the side chain of F75cw is a central hydrophobic contact for the Neu5Ac methyl group. This residue would interfere with the binding of Neu5Ac in the orientation observed in the LPyV VP1 complex. In LPyV VP1, replacement of F75cw with lysine, a different conformation of the BC2cw-loop and a more distant DE-loop create a recessed surface with an especially deep and narrow pocket that can accommodate Neu5Ac. As a consequence of these changes, the conserved residues of the HI-loop engage in different contacts with the two Neu5Ac orientations (Fig. 5). Taken together, the comparison highlights how the architecture of the sialic acid binding site, constructed from several loops, can be varied by mutation of some modules while conserving others. With LPyV, there are four known orientations of sialic acid in polyomavirus binding sites. Except for the LPyV-SV40 pair, none of the amino acids that contact them are conserved, but they tend to occupy equivalent positions in sequence and in structure. The observed partial conservation might be a general strategy for evolving binding sites with new properties through functional intermediates that minimize the risk of losing binding altogether.


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)

Comparison of oligosaccharide binding sites of LPyV and SV40.A & C. LPyV VP1 in complex with 3SL. B & D. SV40 VP1 in complex with GM1 pdb (3BWR). In panels A and B, the proteins are shown in surface representation, with the BC- and HI-loops also indicated in cartoon representation. Residues contributing to ligand binding or specificity are shown in stick representation. Receptor-binding residues that are identical between the two proteins are colored yellow in both panels, while residues that differ between the two proteins, but reside on the same location on the VP1 surface, are colored bright green for LPyV and cyan for SV40. Residues that make additional contacts with the oligosaccharide only in one complex are colored dark green for LPyV and dark blue for SV40. Their non-binding counterparts in the other complex are colored white. The carbohydrate ligands are shown as orange sticks. Hydrogen bonds and water-mediated hydrogen bonds are shown as black and grey dashes, respectively. In panels C and D, the proteins are shown in ribbon presentation, with one monomer highlighted in green for LPyV and blue for SV40 VP1, respectively.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3814675&req=5

ppat-1003714-g005: Comparison of oligosaccharide binding sites of LPyV and SV40.A & C. LPyV VP1 in complex with 3SL. B & D. SV40 VP1 in complex with GM1 pdb (3BWR). In panels A and B, the proteins are shown in surface representation, with the BC- and HI-loops also indicated in cartoon representation. Residues contributing to ligand binding or specificity are shown in stick representation. Receptor-binding residues that are identical between the two proteins are colored yellow in both panels, while residues that differ between the two proteins, but reside on the same location on the VP1 surface, are colored bright green for LPyV and cyan for SV40. Residues that make additional contacts with the oligosaccharide only in one complex are colored dark green for LPyV and dark blue for SV40. Their non-binding counterparts in the other complex are colored white. The carbohydrate ligands are shown as orange sticks. Hydrogen bonds and water-mediated hydrogen bonds are shown as black and grey dashes, respectively. In panels C and D, the proteins are shown in ribbon presentation, with one monomer highlighted in green for LPyV and blue for SV40 VP1, respectively.
Mentions: Despite these differences, the LPyV binding site lies in a region that partially overlaps with the sialic acid binding sites on other polyomaviruses. LPyV engages Neu5Ac in an orientation that resembles that seen in the complex of SV40 VP1 with GM1, and it is therefore useful to compare the two modes of interaction (Fig. 5). Interestingly, the two binding sites are “half-conserved”. The HI-loop, which contributes the “back” wall of the sialic acid binding site, is conserved, while the BC1-, BC2cw- and DE-loops feature marked differences, which explain the different orientations of bound Neu5Ac. In the SV40 VP1 complex, the side chain of F75cw is a central hydrophobic contact for the Neu5Ac methyl group. This residue would interfere with the binding of Neu5Ac in the orientation observed in the LPyV VP1 complex. In LPyV VP1, replacement of F75cw with lysine, a different conformation of the BC2cw-loop and a more distant DE-loop create a recessed surface with an especially deep and narrow pocket that can accommodate Neu5Ac. As a consequence of these changes, the conserved residues of the HI-loop engage in different contacts with the two Neu5Ac orientations (Fig. 5). Taken together, the comparison highlights how the architecture of the sialic acid binding site, constructed from several loops, can be varied by mutation of some modules while conserving others. With LPyV, there are four known orientations of sialic acid in polyomavirus binding sites. Except for the LPyV-SV40 pair, none of the amino acids that contact them are conserved, but they tend to occupy equivalent positions in sequence and in structure. The observed partial conservation might be a general strategy for evolving binding sites with new properties through functional intermediates that minimize the risk of losing binding altogether.

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