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A structure-guided mutation in the major capsid protein retargets BK polyomavirus.

Neu U, Allen SA, Blaum BS, Liu Y, Frank M, Palma AS, Ströh LJ, Feizi T, Peters T, Atwood WJ, Stehle T - PLoS Pathog. (2013)

Bottom Line: We have characterized the receptor specificity, structure and infectivity of the human polyomavirus BKPyV, the causative agent of polyomavirus-associated nephropathy, and uncover a molecular switch for binding different carbohydrate receptors.The crystal structure of the BKPyV capsid protein VP1 in complex with GD3 reveals contacts with two sialic acid moieties in the receptor, providing a basis for the observed specificity.Mutation of this residue from lysine in BKPyV to serine in SV40 switches the receptor specificity of BKPyV from GD3 to GM1 both in vitro and in cell culture.

View Article: PubMed Central - PubMed

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

ABSTRACT
Viruses within a family often vary in their cellular tropism and pathogenicity. In many cases, these variations are due to viruses switching their specificity from one cell surface receptor to another. The structural requirements that underlie such receptor switching are not well understood especially for carbohydrate-binding viruses, as methods capable of structure-specificity studies are only relatively recently being developed for carbohydrates. We have characterized the receptor specificity, structure and infectivity of the human polyomavirus BKPyV, the causative agent of polyomavirus-associated nephropathy, and uncover a molecular switch for binding different carbohydrate receptors. We show that the b-series gangliosides GD3, GD2, GD1b and GT1b all can serve as receptors for BKPyV. The crystal structure of the BKPyV capsid protein VP1 in complex with GD3 reveals contacts with two sialic acid moieties in the receptor, providing a basis for the observed specificity. Comparison with the structure of simian virus 40 (SV40) VP1 bound to ganglioside GM1 identifies the amino acid at position 68 as a determinant of specificity. Mutation of this residue from lysine in BKPyV to serine in SV40 switches the receptor specificity of BKPyV from GD3 to GM1 both in vitro and in cell culture. Our findings highlight the plasticity of viral receptor binding sites and form a template to retarget viruses to different receptors and cell types.

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Structure of a BKPyV VP1-GD3 oligosaccharide complex.(A) Structure of BKPyV VP1 pentamer in complex with GD3 oligosaccharide. One VP1 monomer is highlighted in green. Monosaccharides unbiased by crystal contacts are colored orange, while the ones binding to crystal contacts are colored white. (B) Composite annealed difference electron density for the terminal disialic acid motif of GD3 oligosaccharide bound to BKPyV VP1 at a σ level of 2.5. cw/ccw = belonging to the clockwise/counterclockwise neighboring VP1 monomer within the pentamer. (C) Interactions of GD3 oligosaccharide with BKPyV VP1. The oligosaccharide is shown in orange. Side chains contacting the sugar are colored as follows: those making hydrogen bonds are colored dark green, those making van der Waals interactions are light green, and those making water-mediated hydrogen bonds are colored yellow. Atoms of the protein backbone are shown in gray, and water molecules are in cyan. Direct hydrogen bonds are indicated as black dashed lines, water-mediated ones are grey. (D+E) Model of the interaction of BKPyV VP1 with GD1b oligosaccharide. The left arm and the stem of GD1b are colored orange. Residues interacting with the left arm of GD1b are colored as in (C). The disialic acid motif of GD1b and the protein residues contacting it are colored white.
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ppat-1003688-g002: Structure of a BKPyV VP1-GD3 oligosaccharide complex.(A) Structure of BKPyV VP1 pentamer in complex with GD3 oligosaccharide. One VP1 monomer is highlighted in green. Monosaccharides unbiased by crystal contacts are colored orange, while the ones binding to crystal contacts are colored white. (B) Composite annealed difference electron density for the terminal disialic acid motif of GD3 oligosaccharide bound to BKPyV VP1 at a σ level of 2.5. cw/ccw = belonging to the clockwise/counterclockwise neighboring VP1 monomer within the pentamer. (C) Interactions of GD3 oligosaccharide with BKPyV VP1. The oligosaccharide is shown in orange. Side chains contacting the sugar are colored as follows: those making hydrogen bonds are colored dark green, those making van der Waals interactions are light green, and those making water-mediated hydrogen bonds are colored yellow. Atoms of the protein backbone are shown in gray, and water molecules are in cyan. Direct hydrogen bonds are indicated as black dashed lines, water-mediated ones are grey. (D+E) Model of the interaction of BKPyV VP1 with GD1b oligosaccharide. The left arm and the stem of GD1b are colored orange. Residues interacting with the left arm of GD1b are colored as in (C). The disialic acid motif of GD1b and the protein residues contacting it are colored white.

Mentions: To define the structural features underlying the receptor-binding specificity of BKPyV, we solved the structure of the BKPyV VP1 pentamer at 2.0 Å resolution (Table 1). The VP1 pentamer is a doughnut-shaped ring, with the five monomers arranged around a central pore that aligns with the five-fold symmetry axis (Fig. 2A). The monomers adopt a β-sandwich fold with jelly-roll topology that is present in many viral capsid proteins. The β-strands B, I, D, G and C, H, E, F (designated alphabetically from the N-terminus of the full-length protein) are linked by extensive loops that decorate the surface of the protein. For clarity, the long BC-loop is subdivided into loops BC1 and BC2, which face in different directions.


A structure-guided mutation in the major capsid protein retargets BK polyomavirus.

Neu U, Allen SA, Blaum BS, Liu Y, Frank M, Palma AS, Ströh LJ, Feizi T, Peters T, Atwood WJ, Stehle T - PLoS Pathog. (2013)

Structure of a BKPyV VP1-GD3 oligosaccharide complex.(A) Structure of BKPyV VP1 pentamer in complex with GD3 oligosaccharide. One VP1 monomer is highlighted in green. Monosaccharides unbiased by crystal contacts are colored orange, while the ones binding to crystal contacts are colored white. (B) Composite annealed difference electron density for the terminal disialic acid motif of GD3 oligosaccharide bound to BKPyV VP1 at a σ level of 2.5. cw/ccw = belonging to the clockwise/counterclockwise neighboring VP1 monomer within the pentamer. (C) Interactions of GD3 oligosaccharide with BKPyV VP1. The oligosaccharide is shown in orange. Side chains contacting the sugar are colored as follows: those making hydrogen bonds are colored dark green, those making van der Waals interactions are light green, and those making water-mediated hydrogen bonds are colored yellow. Atoms of the protein backbone are shown in gray, and water molecules are in cyan. Direct hydrogen bonds are indicated as black dashed lines, water-mediated ones are grey. (D+E) Model of the interaction of BKPyV VP1 with GD1b oligosaccharide. The left arm and the stem of GD1b are colored orange. Residues interacting with the left arm of GD1b are colored as in (C). The disialic acid motif of GD1b and the protein residues contacting it are colored white.
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Related In: Results  -  Collection

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ppat-1003688-g002: Structure of a BKPyV VP1-GD3 oligosaccharide complex.(A) Structure of BKPyV VP1 pentamer in complex with GD3 oligosaccharide. One VP1 monomer is highlighted in green. Monosaccharides unbiased by crystal contacts are colored orange, while the ones binding to crystal contacts are colored white. (B) Composite annealed difference electron density for the terminal disialic acid motif of GD3 oligosaccharide bound to BKPyV VP1 at a σ level of 2.5. cw/ccw = belonging to the clockwise/counterclockwise neighboring VP1 monomer within the pentamer. (C) Interactions of GD3 oligosaccharide with BKPyV VP1. The oligosaccharide is shown in orange. Side chains contacting the sugar are colored as follows: those making hydrogen bonds are colored dark green, those making van der Waals interactions are light green, and those making water-mediated hydrogen bonds are colored yellow. Atoms of the protein backbone are shown in gray, and water molecules are in cyan. Direct hydrogen bonds are indicated as black dashed lines, water-mediated ones are grey. (D+E) Model of the interaction of BKPyV VP1 with GD1b oligosaccharide. The left arm and the stem of GD1b are colored orange. Residues interacting with the left arm of GD1b are colored as in (C). The disialic acid motif of GD1b and the protein residues contacting it are colored white.
Mentions: To define the structural features underlying the receptor-binding specificity of BKPyV, we solved the structure of the BKPyV VP1 pentamer at 2.0 Å resolution (Table 1). The VP1 pentamer is a doughnut-shaped ring, with the five monomers arranged around a central pore that aligns with the five-fold symmetry axis (Fig. 2A). The monomers adopt a β-sandwich fold with jelly-roll topology that is present in many viral capsid proteins. The β-strands B, I, D, G and C, H, E, F (designated alphabetically from the N-terminus of the full-length protein) are linked by extensive loops that decorate the surface of the protein. For clarity, the long BC-loop is subdivided into loops BC1 and BC2, which face in different directions.

Bottom Line: We have characterized the receptor specificity, structure and infectivity of the human polyomavirus BKPyV, the causative agent of polyomavirus-associated nephropathy, and uncover a molecular switch for binding different carbohydrate receptors.The crystal structure of the BKPyV capsid protein VP1 in complex with GD3 reveals contacts with two sialic acid moieties in the receptor, providing a basis for the observed specificity.Mutation of this residue from lysine in BKPyV to serine in SV40 switches the receptor specificity of BKPyV from GD3 to GM1 both in vitro and in cell culture.

View Article: PubMed Central - PubMed

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

ABSTRACT
Viruses within a family often vary in their cellular tropism and pathogenicity. In many cases, these variations are due to viruses switching their specificity from one cell surface receptor to another. The structural requirements that underlie such receptor switching are not well understood especially for carbohydrate-binding viruses, as methods capable of structure-specificity studies are only relatively recently being developed for carbohydrates. We have characterized the receptor specificity, structure and infectivity of the human polyomavirus BKPyV, the causative agent of polyomavirus-associated nephropathy, and uncover a molecular switch for binding different carbohydrate receptors. We show that the b-series gangliosides GD3, GD2, GD1b and GT1b all can serve as receptors for BKPyV. The crystal structure of the BKPyV capsid protein VP1 in complex with GD3 reveals contacts with two sialic acid moieties in the receptor, providing a basis for the observed specificity. Comparison with the structure of simian virus 40 (SV40) VP1 bound to ganglioside GM1 identifies the amino acid at position 68 as a determinant of specificity. Mutation of this residue from lysine in BKPyV to serine in SV40 switches the receptor specificity of BKPyV from GD3 to GM1 both in vitro and in cell culture. Our findings highlight the plasticity of viral receptor binding sites and form a template to retarget viruses to different receptors and cell types.

Show MeSH
Related in: MedlinePlus