Results: 4

1.
Figure 3

Figure 3. Sequence alignment of the flaviviral NS4A. From: Structural and functional parameters of the flaviviral protease: a promising antiviral drug target.

The acidic C-terminal motif is in a frame. The 44–53 acidic motif of HCV NS4A is shown below the alignment. Homologous residues are in gray. Dots indicate identical residues.
DV: Dengue virus; JEV: Japanese encephalitis virus; KV: Kunjin virus; WNV: West Nile virus; YFV: Yellow fever virus.

Sergey A Shiryaev, et al. Future Virol. ;5(5):593-606.
2.
Figure 1

Figure 1. Organization of the capsid–membrane–envelope–NS1–NS2A–NS2B–NS3–NS4A–NS4B–NS5 polyprotein precursor, showing cleavage sites by the viral NS2B–NS3pro (gray arrows) and host cell secretase and furin (black arrows), with detail of the NS2B and NS3 sequences. From: Structural and functional parameters of the flaviviral protease: a promising antiviral drug target.

The hydrophilic central region of the NS2B cofactor is gray. The West Nile virus residue numbering is shown above the polyprotein structure.
C: Capsid; E: Envelope; M: Membrane; NS: Nonstructural; TM: Transmembrane domain.

Sergey A Shiryaev, et al. Future Virol. ;5(5):593-606.
3.
Figure 4

Figure 4. Structure of the West Nile virus NS2B–NS3pro. From: Structural and functional parameters of the flaviviral protease: a promising antiviral drug target.

(A) Aprotinin-bound NS2B–NS3pro with secondary structural elements and N- and C-termini indicated. The N- and C-terminal lobes of NS3 are green and gray, respectively. NS2B and aprotinin are purple and yellow, respectively. The linker between the two lobes is orange. The catalytic triad is shown as black balls. The localization of the structural elements in the peptide sequence is shown in Figure 2. (B) Two conformations of the NS2B cofactor. Superposition of WNV NS2B–NS3 proteases: substrate-free (green and blue) and aprotinin-bound (gray and red). The secondary elements of NS2B unique to the substrate-free (α1 and β1′) and the substrate-bound (β2 and β3) structures, as well as the alternative C-termini are indicated. The point of departure (Trp62) for the two NS2B elements is labeled and shown as a stick model. The elements β2′ and β3′ in the substrate-free structure are stabilized by crystal contacts.

Sergey A Shiryaev, et al. Future Virol. ;5(5):593-606.
4.
Figure 2

Figure 2. NS3 sequences of the flaviviruses. From: Structural and functional parameters of the flaviviral protease: a promising antiviral drug target.

(A) Sequence alignment of the NS3pro domain. Sections highlighted in red indicate identity; red letters indicate homology. Secondary structure elements above the sequences are for the WNV NS2B–NS3pro; those below are for the HCV NS3pro–NS4A (PDB entry 1JXP). Gray rectangles highlight regions where the folds of the WNV NS2B–NS3pro and the HCV NS3pro-NS4A differ. The residues of the Asp-His-Ser catalytic triad are indicated by green asterisks. (B) Sequence alignment of flaviviral NS2B and HCV NS4A. Boxes indicate minimal cofactor segments required for activation of NS3pro in vitro. TM1–TM4 are predicted transmembrane regions. Hydrophobic and aromatic residues are green, polar are black, acidic in red and basic in blue. Secondary structure elements are for the WNV NS2B–NS3pro–aprotinin complex; the alternate elements (α1 and β19) found in the inhibitor-free WNV and DV NS2B–NS3pro are drawn with dotted lines.
DV: Dengue virus; JEV: Japanese encephalitis virus; KV: Kunjin virus; TM: Transmembrane; WNV: West Nile virus; YFV: Yellow fever virus.

Sergey A Shiryaev, et al. Future Virol. ;5(5):593-606.

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