Results: 5

1.
Fig. 1.

Fig. 1. From: Structural Analysis of Histo-Blood Group Antigen Binding Specificity in a Norovirus GII.4 Epidemic Variant: Implications for Epochal Evolution.

Multiple-sequence alignment of representative GII.4 variants from 1995 to 2010. Only residues from aa 331 to 450 in the P domain of the capsid protein are shown. Amino acid residues in site 1 are highlighted in yellow. Site 2 with temporally evolving residues is highlighted in cyan. The I-to-V changes at position 389 are highlighted in green. The amino acid sequences of 1996 (VA387) and 2004 (TCH05) GII.4 variants are shown in red. Every 10th residue is denoted by a dot above the sequences. A sequence similarity index is shown below the sequences according to ClustalW conventions (asterisk, invariant; colon, highly similar; dot, similar). GenBank accession numbers for the various sequences represented here are as follows: X86557 for Lordsdale, AJ004864 for 1995_96, AB294779 for 2001Japan, EU310927 for 2001Henry, AY485642 for 2002; AB220922 for 2003Asia, JF827296 for 2004, EF126963 for 2006a, EF126965 for 2006b, AB445395 for 2008 Apeldoorn 317/2007, and GU445325 for 2010 New Orleans 1805/2009.

Sreejesh Shanker, et al. J Virol. 2011 September;85(17):8635-8645.
2.
Fig. 4.

Fig. 4. From: Structural Analysis of Histo-Blood Group Antigen Binding Specificity in a Norovirus GII.4 Epidemic Variant: Implications for Epochal Evolution.

Binding of difucosyl Lewis HBGA to the 2004 P domain dimer. (A) Surface representation (top view) showing a close-up view of one of the two binding sites in the 2004 P domain dimer bound to Leb hexasaccharide. The coloring scheme for the amino acid residues in site 1 and site 2 is the same as that described in the legend of Fig. 3A. The individual saccharide moieties in the Leb hexasaccharide are labeled SeFuc (secretor fucose), LeFuc (Lewis fucose), βGal (galactose), GlcNAc (N-acetylglucosamine), and Glc (glucose). (B) Detailed interactions of the Leb hexasaccharide with the 2004 P domain. P domain residues participating in the hydrogen-bonding (black dashed lines) and hydrophobic (red dotted lines) interactions with Leb (individual moieties denoted as described above) are labeled and shown as pink (site 1) and green (site 2) sticks, with nitrogen and oxygen atoms in blue and red, respectively. The water molecule involved in solvent-mediated interactions with residue Y444′ and O6 of GlcNAc is labeled W and is shown as a red sphere. (C) Close-up view of the superposition of site 2 from the 1996 variant (cyan) with the Leb-bound 2004 variant (orange). Dashed lines represent hydrogen-bonding interactions between site 2 residues of the 2004 variant and the Lewis fucose of Leb. The site 2 residues in the 2004 variant participating in hydrogen-bonding interactions are shown as orange sticks, with nitrogen and oxygen atoms labeled in blue and red, respectively. Their counterparts in the 1996 strain are shown as cyan sticks. Because of the structural alterations in site 2 of the 1996 variant, similar hydrogen-bonding interactions with Leb involving site 2 residues are not possible.

Sreejesh Shanker, et al. J Virol. 2011 September;85(17):8635-8645.
3.
Fig. 5.

Fig. 5. From: Structural Analysis of Histo-Blood Group Antigen Binding Specificity in a Norovirus GII.4 Epidemic Variant: Implications for Epochal Evolution.

Comparison of P domain monomers and dimers. (A) Cartoon representation of the P domain monomer in the C2 crystal form (yellow). Site 1 residues are shown in magenta for reference. (B) Cartoon representation of the P domain dimer in the C2221 crystal form. The dimeric subunits are indicated in purple and gray, and black arrows indicate the location of the HBGA binding sites. HBGA binding sites 1 and 2 are indicated in magenta and green, respectively. (C) Cartoon representation of the P domain monomer in the C2221 crystal form (cyan). Site 1 residues are shown in magenta for reference. (D) Superposition of the C2 monomer (yellow) and one of the dimer subunits (purple) in the C2221 crystal form. Regions with conformational flexibility, which include site 1, are shown inside a box (side view). The inset shows the top view of this boxed loop region. Site 2 (green) is seen only in the dimer subunit (purple); this region in the C2 monomer is disordered. Arrows indicate the HBGA binding sites. (E) Superposition of the C2221 monomer (cyan) and a subunit from the dimer (purple) in the same C2221 crystal form. Regions with conformational flexibility, which include site 1, are shown inside a box (side view). The top view of this boxed region is shown in the inset. As in D, site 2 (green) is seen only in the dimer subunit (purple), and this region in the C2221 monomer is disordered. Arrows indicate the HBGA binding region. (F) Cation-π interaction between residues H396 and Y444 in the P domain of the 2004 variant with a face-to-face distance of ∼3.8 Å (indicated by a red dashed line). These two highly conserved residues are in close proximity to the dimeric interface, HBGA binding sites 1 (magenta) and 2 (green). Bound H-type HBGA is shown (yellow) for reference. The cation-π interaction is observed only for the dimeric subunits and is not observed for the monomeric state, as the loops containing residues H396 and Y444 in this state are disordered.

Sreejesh Shanker, et al. J Virol. 2011 September;85(17):8635-8645.
4.
Fig. 3.

Fig. 3. From: Structural Analysis of Histo-Blood Group Antigen Binding Specificity in a Norovirus GII.4 Epidemic Variant: Implications for Epochal Evolution.

Binding of monofucosyl ABH family HBGAs to the 2004 P domain dimer. (A) Surface representation (top view) showing a close-up view of one of the two binding sites in the 2004 P domain dimer bound to an A-type trisaccharide. Identical interactions with the trisaccharide were observed for the other binding site of the dimer and are not shown. Amino acid residues in site 1 and site 2 are shown in pink and green, respectively, with other residues from the dimeric subunits in the vicinity shown as blue and cyan. The HBGAs, here and in all subsequent figures, are shown as yellow sticks, with nitrogen atoms and oxygen atoms shown in blue and red, respectively. The individual saccharide moieties in the A-type trisaccharide are labeled as Fuc (fucose), βGal (galactose), and GalNAc (N-acetylgalactosamine). (B) Detailed interactions of the A-type trisaccharide with the 2004 P domain dimer. P domain residues participating in the hydrogen-bonding (black dashed lines) and hydrophobic (red dotted lines) interactions with the trisaccharide are labeled and shown as pink sticks, with nitrogen and oxygen atoms in blue and red, respectively; the rest of the dimer is shown as a cartoon representation. The individual moieties of the trisaccharide are labeled as described above (A). The water molecule involved in solvent-mediated interactions with site 2 is labeled W and is shown as a red sphere. (C) Surface representation (top view) showing a close-up view of one of the two binding sites in the 2004 P domain dimer bound to the H-type pentasaccharide. Amino acid residues in site 1 and site 2 are colored as described above (A). The H-type pentasaccharide is shown as stick model with individual moieties labeled as Fuc (fucose), βGal (galactose), GlcNAc (N-acetylglucosamine), and Glc (glucose). (D) Detailed interactions of the H-type pentasaccharide with the 2004 P domain. P domain residues participating in the hydrogen-bonding (black dashed lines) and hydrophobic (red dotted lines) interactions with the pentasaccharide (individual moieties labeled as described above) are labeled and shown as pink sticks, with nitrogen and oxygen atoms in blue and red, respectively. The individual moieties of the pentasaccharide are labeled as described above (C).

Sreejesh Shanker, et al. J Virol. 2011 September;85(17):8635-8645.
5.
Fig. 2.

Fig. 2. From: Structural Analysis of Histo-Blood Group Antigen Binding Specificity in a Norovirus GII.4 Epidemic Variant: Implications for Epochal Evolution.

Structural comparison of P domain dimers of 2004 and 1996 GII.4 variants. (A) Superposition of the 2004 (orange) and 1996 (cyan) P domain dimer structures. The N and C termini of the dimeric subunits in the 2004 P domain structure are indicated. HBGA binding sites observed for the 1996 variant structure are indicated by arrows. Red and black boxes indicate locations of site 1 and site 2, respectively, in the P domain dimer. A conformational change in the site 2 loop (black box) between the two variants is clearly evident. The alignment of residues in site 1 and site 2 of the 1996 and 2004 GII.4 variants is shown below. (B and C) Side-by-side comparison of the electrostatic potential surfaces of the 2004 and 1996 P domain dimers. (B) Side (above) and top (below) views of the 2004 variant. (C) Side (above) and top (below) views of the 1996 variant. The electrostatic potential variation from negative (red) to positive (blue) is indicated by a bar at the bottom. Significant differences in the electrostatic potential surfaces between the variants are indicated by colored dashed arrows, with each color representing a different region. The temporally varying residues that contribute to these changes are also indicated. For reference, the locations of the HBGA binding sites in the P domain dimer are indicated by black arrows in the side views and by black boxes in the top views. Residues 340 (pink), 393 to 395 (black), and 412 (blue) have all been identified as hot spots for GII.4 epochal evolution.

Sreejesh Shanker, et al. J Virol. 2011 September;85(17):8635-8645.

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