Structure of the Vesicular Stomatitis Virus N0-P Complex
Figure 5
Surface properties and amino acid conservation in the P binding site.
(A) Close up of the interface between RNA-free NΔ21 and P60 showing the hydrophobic contacts and salt bridges. Residues 17 to 31 of P60 fold into an amphipathic α-helix that lies in a hydrophobic cavity formed by residues of the hinge region of N and is stabilized by hydrophobic contacts involving residues of P60 spaced i+3 or i+4 (Leu17, Val21, Ile24 and Ile27). Tyr14 docks into a small cavity lined with hydrophobic residues. Hydrophobic side chains in N are colored in yellow and hydrophobic side chains of P60 are labeled. The complex is also stabilized by salt bridges between Asp25 of P60 and Arg312 and His233 of N (in blue) and between Arg16 of P60 and Asp269 of N (in red). (B) Amino acid sequence conservation between VSV and RAV N. Identical residues are shown in dark blue and similar residues are shown in light blue. The surface area circled in black shows the binding groove of P and the surface area circle in red shows the hydrophobic site common to both P and the bases at the 3′ end of the RNA. (C, D) Electrostatic surface potential of the NΔ210 protein (C) compared with that of the NΔ210-P60 complex (D). Both panels show in the same orientations the two sides of the NΔ210 protein involved in binding the MoRE of P. The arrows indicate regions in which the electrostatic surface potential of N is modified by the presence of the peptide. The surface potentials were calculated with the Delphi program and are color-coded on the surface from red (negatively charged residues, −7 kcal/mol) to blue (positively charged residues, +7 kcal/mol).